R/app_ui.R
In cparsania/FungiExpresZ: FungiExpresZ: Fungal gene expression data analysis and visualizations
Defines functions
golem_add_external_resources
app_ui
Documented in
app_ui
#' app_ui
#' @import ggplot2
#' @import png
#' @import ggridges
#' @import wordcloud
#' @import clusterProfiler
#' @import shinycssloaders
#' @import ggcorrplot
#' @import prettydoc
#' @import svglite
#' @import circlize
#' @import GGally
#' @import ggfortify
#' @import ggrepel
#' @import ComplexHeatmap
#' @import shinyWidgets
#' @import ggpubr
#' @import shiny
#' @import golem
#' @import htmltools
#' @import processx
#' @import attempt
#' @import shinythemes
#' @import viridis
#' @import formattable
#' @import colourpicker
#' @import ggalt
#' @import gtools
#' @import shinyBS
#' @importFrom scales hue_pal
#' @importFrom shinyjs hide
#' @importFrom shinyjs show
#' @importFrom shinyjs enable
#' @importFrom shinyjs disable
#' @importFrom shinyjs useShinyjs
#' @importFrom DT renderDataTable
#' @importFrom DT dataTableProxy
#' @importFrom DT selectRows
#' @importFrom DT dataTableOutput
#' @importFrom DT JS
#' @importFrom DT datatable
#' @importFrom badger ver_devel
#'
#' @keywords internal
#'
app_ui <- function() {
tagList(
# Leave this function for adding external resources
golem_add_external_resources(),
# List the first level UI elements here
fluidPage(
#tags$head(includeScript("./google_analytics.js")),
#tags$head(includeScript("./inst/app/www/google_analytics.js")),
#tags$head(includeScript("www/google_analytics.js")),
theme = shinythemes::shinytheme("flatly"),
shinyjs::useShinyjs(),
## import google fonts
tags$head(
tags$style(HTML("
@import url('https://fonts.googleapis.com/css?family=Ribeye&display=swap'
"))
),
## arrange title panel
tags$div(
#tags$a(img(src="https://raw.githubusercontent.com/cparsania/FungiExpresZ/master/inst/app/www/hex_sticker.png" , height="150")),
titlePanel(
tags$h1("Fungi",
tags$a(img(src="https://raw.githubusercontent.com/cparsania/FungiExpresZ/master/inst/app/www/hex_sticker.png" , height="100"),
href = "https://raw.githubusercontent.com/cparsania/FungiExpresZ/master/inst/app/www/hex_sticker.png" , target= "_blank"),
"ExpresZ",
tags$h2("Fungal Gene Expression Data Analysis and Visualization Tool" , style = "font-family: 'Ribeye'") ,
align = "center",
style = "font-family: 'Ribeye'; font-size: 80px;"
),
windowTitle = "FungiExpresZ") ,
style = "color:white;
background-color:#2C3E50;
text-align: center;
padding: 5px 0 "),
# CSS reference : https://stackoverflow.com/questions/28630433/how-to-align-navbar-to-center-with-css
## adjust navbar panel
tags$style(HTML("
ul.nav.navbar-nav {
left: 0px;
width: 100%;
display: flex;
justify-content: center;
}")),
#navbar navbar-default navbar-static-top
navbarPage(collapsible = T,fluid = T,
title = "",
tabPanel(title = "App", icon = icon("home"),
sidebarLayout(
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## UI sidebar panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
sidebarPanel(
width = 3,
h2("Inputs"),
## upload data
shinyBS::bsCollapse(
open = c("Select / Upload data" , "Assign Groups"),
multiple = T,
shinyBS::bsCollapsePanel(
title = "Select / Upload data", style = "primary",
radioButtons(inputId = "data_selection",
label = "",
choices = c("Select data" = "select_sample",
"Upload / Use example data" = "upload_user_data"),
inline = F),
## select data action button
conditionalPanel(
condition = "input.data_selection =='select_sample'",
shinyWidgets::actionBttn(
inputId = "select_sample_trigger",
label = "Select", color = "success",
style = "gradient", size = "md",
icon = icon("database"), block = T
)
),
## Select datatrigger
shinyBS::bsModal(
id = "trigger_select_sample_data",
title = fluidRow(
fluidRow(column(11, offset = 1,tags$h2(tags$b("Sequence Read Archive (SRA) Run Inforamation Table"))))
),
trigger = "select_sample_trigger",
size = "large",
## row having selection instruction
fluidRow(
column (
width = 12,
tags$h3(tags$b("Click on row(s) to select SRA samples for analysis and visualisation.", tags$br() , tags$br(), "Once selection made click submit."))
)
),
hr(),
## row having row filter title
fluidRow(
column(
width = 4,
offset = 5,
tags$h2(tags$b("Row filters"))
)
),
### row having filer buttons
fluidRow(
column(
width = 4,
## Species
shinyWidgets::pickerInput(
inputId = "select_species",
selected = "Aspergillus nidulans",
label = "Organism",
choices = NULL,
choicesOpt = T,
width = "100%",
options = list(
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", "max-options" = 1, `live-search` = TRUE
)
)
),
## Strain
column(
width = 4,
shinyWidgets::pickerInput(
inputId = "select_strain",
label = "Strain",
choices = NULL,
choicesOpt = F,
selected = "",
multiple = T,
width = "100%",
options = shinyWidgets::pickerOptions(liveSearch = TRUE,
size = 10 ,
selectedTextFormat = "count > 10" ,
maxOptions = 1,
style = "btn-success")
)
),
## Genotype
column(
width = 4,
shinyWidgets::pickerInput(
inputId = "select_genotype",
label = "Genotype",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = shinyWidgets::pickerOptions(liveSearch = TRUE,
size = 10 ,
selectedTextFormat = "count > 10" ,
maxOptions = 1,
style = "btn-success")
)
)
),
## reset filters
fluidRow(
column(width = 4,
offset = 4,
## reset strain
shinyWidgets::actionBttn(
inputId = "reset_strain_filter",
label = "",
icon = icon("sync-alt"),
color ="success",
style ="gradient",
size = "sm"
)
),
column(width = 4,
#reset genotype
shinyWidgets::actionBttn(
inputId = "reset_genotype_filter",
label = "",
icon = icon("sync-alt"),
color = "success",
style ="gradient",
size = "sm"
)
)
),
hr(),
## select all rows
shinyWidgets::checkboxGroupButtons(
inputId = "sra_sample_info_select_all_rows",
label = "",
choices = c("Select all rows" = TRUE),
status = "success",selected = FALSE,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
br(), br(),
## SRA info table
div(DT::dataTableOutput(outputId = "pre_loaded_data_sra_sample_info" , width = "auto") %>%
shinycssloaders::withSpinner(color = "#18BC9C") , style = "font-size:80%"),
br(), br(),
## Display number of rows selected
fluidRow(
column(width = 12,offset =5,
tags$h3(tags$b(textOutput(outputId = "sra_info_number_of_rows_selected")))
)
),
br(), br(),
fluidRow(
## clear all
column(width = 4,offset = 3,
shinyWidgets::actionBttn(inputId = "deselect_all_rows",
label = "Clear all" ,
size = "md" ,
style = "gradient",
icon = icon("times-circle"),
color = "success")
),
## submit
column(width = 4,
shinyWidgets::actionBttn(inputId = "submit_user_sra_samples",
label = "Submit" ,
size = "md",
style = "gradient" ,
icon = icon("thumbs-up"),
color = "success")
)
)
),
## upload data action button
conditionalPanel(
condition = "input.data_selection =='upload_user_data'",
shinyWidgets::actionBttn(
inputId = "upload_sample_trigger",
label = "Upload", color = "success",
style = "gradient", size = "md",
icon = icon("upload"), block = T
)
),
## upload data trigger
shinyBS::bsModal(size = "large",
id = "trigger_upload_user_data", title = "Upload Data",
trigger = "upload_sample_trigger",
## upload sample data checkbox
shinyWidgets::materialSwitch(
inputId = "upload_sample_data",
label = tags$b("Upload example data"),
value = FALSE,
status = "info"
),
shinyWidgets::progressBar(id = "upload_sample_data_pb", value = 0, status = "success", striped = TRUE),
hr(),
##upload data, either from file or from clipboard
tags$div(id = "user_data_upload_section",
tags$h2(tags$b("Step 1: Upload data")),
wellPanel(
fluidRow(
column(width = 12,
radioButtons(inputId = "upload_data_source" , label = "",
choices = c("From file" = "upload_from_file", "From clipboard" = "upload_from_clipboard"),
width = "100%",inline = T,
)
)
),
fluidRow(
conditionalPanel(condition = "input.upload_data_source == 'upload_from_file'",
column(width = 12,
fileInput(
inputId = "file1",
label = "",
#label = tags$h3(tags$b("Read from file")), #"Choose .txt file",
multiple = F,width = "100%",placeholder = "Upload .txt file",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv"
)
)
)
),
conditionalPanel(condition = "input.upload_data_source == 'upload_from_clipboard'",
column(width = 12,
textAreaInput(placeholder = "Paste data here",
inputId = "user_pasted_data",
label = "",cols = 10, rows = 10
#label = tags$h3(tags$b("Read from file")), #"Choose .txt file",
#multiple = F,width = "100%",placeholder = "Upload .txt file",
)
)
)
),
tags$div(id = "file_instruct", tags$h4(tags$b("Data uploading instructions")), "While uploding data from file, file must be of .txt format. Columns are variables (e.g. sample names) and rows are observations (e.g. genes). Each column and row must have unique identity given as first row and first column respectively. Same rules also appy while pasting data from clipboard.")
),
## choice of column seperator
tags$h2(tags$b("Step 2: Select column separator")),
wellPanel(
radioButtons(
inputId = "sep",
label = "",
width = "100%",
choices = c(
Comma = ",",
Semicolon = ";",
Tab = "\t"
),
selected = "\t",
inline = T
)
),
## select species
tags$h2(tags$b("Step 3: Select species (optional)")),
tags$h5(tags$i(
"Corrrect species selection is required for gene annotations and GO analysis."
)),
br(),
wellPanel(
shinyWidgets::pickerInput(
inputId = "user_selected_species",
label = "",
choices = rlang::set_names(species_table$genome , species_table$species),
selected = "FungiDB-66_AnidulansFGSCA4",
choicesOpt = list(
style = "btn-primary",
subtext = species_table$genome),
options = list(`showSubtext` = TRUE)
),
## show random gene id for selected species
tags$div( tags$h4(tags$b("Values in the first column of file being uploaded must have below id type :")) ,
textOutput(outputId = "sample_selected_species_gene_id") %>%
shinycssloaders::withSpinner(color = "#18BC9C"))
),
## log transformation
tags$h2(tags$b("Step 4: Log transformation (optional)")),
wellPanel(
radioButtons(inputId = "log_transform_user_upload_data" ,
label = "",
choices = c("None" = "none" ,
"Log2(value + 1)" = "log2" ,
"Log10(value + 1)" = "log10"),
selected = "none",inline = T
)
),
# decide whether user data to join with existing data
tags$h2(tags$b("Step 5: Join data (optional)")),
wellPanel(
shinyWidgets::materialSwitch(
inputId = "join_user_data",
label = ,
value = FALSE,
status = "success"
),
## join data
tags$div(id = "join_data_instruction",
tags$b("Join data"),
"feature allows users to merge user uploaded data with pre existing data if selected any. Uploaded dataset will be merge by gene names given in the first column."),
br()
),
## submit
fluidRow(
column(width = 4 , offset = 5,
shinyWidgets::actionBttn(inputId = "submit_user_uploaded_data" ,
label = "Submit" ,
icon = icon("thumbs-up") ,
style = "gradient",
color = "success" ,
size = "md" ,
block = F)
)
)
)
)
)
),
hr(),
## Assign groups
shinyBS::bsCollapse(id = "assing_gene_groups_and_sample_groups",
open = "Assign groups",
shinyBS::bsCollapsePanel(title = "Assign groups", style = "primary",
add_sample_group_ui(id = "sample_group"),
br(),
add_gene_groups_ui(id = "gene_groups")
)
),
hr(),
## Display active group info in the side panel
conditionalPanel(condition = "true" ,
shinyBS::bsCollapse(id = "display_active_group_collapse_panel",
open = "View active groups",
shinyBS::bsCollapsePanel(title = "View active groups",
style = "primary" ,
display_active_groups_ui(id = "display_active_groups")
)
)
),
## Display user selected sra id sample info
conditionalPanel(condition = "output.display_sra_sample_info_in_side_panel==true" ,
shinyBS::bsCollapse(id = "display_sra_sample_info_collapse_panel",
open = "View SRA sample info",
shinyBS::bsCollapsePanel(title = "View SRA sample info",
style = "primary",
display_sra_sample_info_ui(id = "user_selected_sra_id_sample_info")
)
)
),
br(),
## display website statistics in side panel
shinyBS::bsCollapse(id = "display_live_statistics",
open = "Usage",
shinyBS::bsCollapsePanel(title = "Usage",
style = "primary",
tags$div(
HTML("<script type=\"text/javascript\" src=\"//rf.revolvermaps.com/0/0/7.js?i=5cen61amuqv&m=0&c=ff0000&cr1=ffffff&sx=0\" async=\"async\"></script>")
)
)
)
## upload data ends
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## UI main panel
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
mainPanel(
width = 9,
tabsetPanel(
type = "tabs",
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## scatter plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Scatter plot", value = "scatter_plot_panel", id = "scatter_plot_panel",
## select plot varibale
h3(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
multiple = T, open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select plot variable
fluidRow(
column(width = 6,
## select x variable
shinyWidgets::pickerInput(
inputId = "scatter_x",
label = "Select sample (X-axis)",
choices = NULL,
choicesOpt = F,
selected = "",
multiple = F, width = "100%",
options = list(
`actions-box` = TRUE,
style = "btn-success", `live-search` = TRUE
)
)
),
column(width = 6,
## select y variable
shinyWidgets::pickerInput(
inputId = "scatter_y",
label = "Select sample (Y-axis)",
choices = NULL, choicesOpt = F,
selected = "", multiple = F, width = "100%",
options = list(
`actions-box` = TRUE,
style = "btn-success", `live-search` = TRUE
)
)
)
),
## select gene groups
gene_group_selection_ui(id = "scatter_plot_select_gene_groups"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_scatter" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
# plot output
conditionalPanel(
condition = "input.generate_scatter && output.scatter_plot_status==true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty column
column(
width = 8,
plotOutput(outputId = "scatter_plot",
brush = "plot_brush", height = "auto", width = "auto")
),
column(width = 2) ## empty column
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## scatter plot advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
hr(),
# column(width = 1), ## empty column
column(
#offset = 1,
width = 12,
## scatter plot Labels & Title button
column(
width = 6,
plot_title_and_axis_label_ui(id = "scatter_plot_title_and_labels")
),
## scatter plot Advance options
column(
width = 3,
shinyWidgets::dropdownButton(
inputId = "scatter_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
h4(tags$b("Axis limits")),
actionLink(
inputId = "trigger_scatter_xy_limits", label = "Set",
icon = icon(name = "edit", lib = "font-awesome")
),
hr(),
## scatter plot trend line
shinyWidgets::radioGroupButtons(
inputId = "scatter_diagonal_line",
label = h4(tags$b("Trend line")),
choices = c(
"Off" = "off",
"From data" = "from_data",
"Manual" = "manual"
),
individual = TRUE ,
justified = T, width = "400px",
status = "success" ,
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## manual slope
conditionalPanel(
condition = "input.scatter_diagonal_line == 'manual'",
fluidRow(
column(
width = 6,
numericInput(inputId = "manual_slope", label = h4(tags$b("Slope")), value = 1)
),
column(
width = 6,
numericInput(inputId = "manual_intercept", label = h4(tags$b("Intercept")), value = 0)
)
)
),
hr(),
# color selection
shinyWidgets::radioGroupButtons(
inputId = "scatter_color_chooser",
label = h4(tags$b("Color by")), choices = c("Density" = "default",
"Manual" = "manual" ,
"Gene group"="by_gene_groups"),
individual = TRUE ,
justified = T , width = "400px",
status = "success" ,size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## color : low
conditionalPanel(
condition = "input.scatter_color_chooser == 'manual'",
fluidRow(
column(
width = 4,
colourpicker::colourInput(
inputId = "scatter_col_low",
label = "low",
value = "blue",
returnName = TRUE
)
),
## color : med
column(
width = 4,
colourpicker::colourInput(
inputId = "scatter_col_medium",
label = "med",
value = "yellow",
returnName = TRUE
)
),
## color : high
column(
width = 4,
colourpicker::colourInput(
inputId = "scatter_col_high",
label = "high",
value = "red",
returnName = TRUE
)
)
)
),
hr(),
## transparancy
sliderInput(
inputId = "scatter_alpha",
label = h4(tags$b("Transparency")), min = 0, max = 1, value = 0.5, step = 0.01, width = "99%"
),
hr(),
## adjust dot size
sliderInput(
inputId = "scatter_point_size",
label = h4(tags$b("Point size")), min = 1, max = 10, value = 2, step = 0.1,width = "99%"
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_scatter")
)
)
)
)
),
### Triggered actions
## set X-Y limits
shinyBS::bsModal(
id = "scatter_xy_limits", title = "Set axis limits", trigger = "trigger_scatter_xy_limits",
column(
width = 6,
## X-lim
numericInput(inputId = "plot_xmin", label = "X-Min:", value = ""),
numericInput(inputId = "plot_xmax", label = "X-Max:", value = "")
),
column(
width = 6,
## Y-lim
numericInput(inputId = "plot_ymin", label = "Y-Min:", value = ""),
numericInput(inputId = "plot_ymax", label = "Y-Max:", value = "")
)
)
### set X-Y limits ends
),
## scatter plot table output
conditionalPanel(
condition = "output.scatter_plot && input.plot_brush",
#downloadButton(outputId = "download_scatter_data", label = "", icon = icon("download")),
## scatter plot data or functional analysis
radioGroupButtons(
inputId = "scatterplot_data_or_functional_analysis",
choices = c("Show Data" = "show_scatterplot_data",
"Functional Analysis" = "scatterplot_functional_analysis"),
status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon")) ,
size = "normal" ,
direction = "horizontal" ,
justified = TRUE ,
individual = TRUE ,selected = "",
width = "100%"
),
br(),
## show scatter plot brushed data
conditionalPanel(
condition = "input.scatterplot_data_or_functional_analysis == 'show_scatterplot_data'",
shinyBS::bsCollapse(
open = "Selected points",
shinyBS::bsCollapsePanel(
title = "Selected points", style = "primary",
DT::dataTableOutput(outputId = "brush_table", width = "auto") %>%
shinycssloaders::withSpinner( color = "#18BC9C")
)
)
),
## show scatter plot functional analysis
conditionalPanel(
condition = "input.scatterplot_data_or_functional_analysis == 'scatterplot_functional_analysis'",
shinyBS::bsCollapse(
open = "Functional analysis",
shinyBS::bsCollapsePanel(
title = "Functional analysis", style = "primary",
functional_analysis_ui(id = "scatterplot_functional_analysis_ui")
)
)
)
)
),
## scatter plot tab panel ends
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## multi scatter plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Multi-scatter plot", value = "multi_scatter_plot_panel", id = "multi_scatter_plot_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
# select plot variables
shinyWidgets::pickerInput(
inputId = "multi_scatter_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
# select gene groups
gene_group_selection_ui("multi_scatter_plot_gene_group_selection"),
## plot action
# actionButton(
# inputId = "generate_multi_scatter",
# label = "Plot"
# )
hr(),
## plot action
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_multi_scatter" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
conditionalPanel(
condition = "input.generate_multi_scatter && output.multi_scatter_plot_status==true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty column
column(
width = 8,
plotOutput(outputId = "multi_scatter_plot", height = "auto", width = "auto")
),
column(width = 2) ## empty column
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## multi scatter plot advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
hr(),
# column(width = 1), ## empty column
column(
width = 12,
## multi scatter labels and Titles
column(
width = 6,
plot_title_and_axis_label_ui(id = "multi_scatter_plot_title_and_labels")
),
## multi scatter Advance options
column(
width = 3,
dropdownButton(
inputId = "multi_scatter_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
## corr text color
colourpicker::colourInput(
inputId = "multi_scatter_corr_text_col",
label = tags$h4(tags$b("Corr text color")),
value = "red",
returnName = TRUE,
palette = "limited"
),
## corr text font size
sliderInput(
inputId = "multi_scatter_corr_text_text_size", label = tags$h4(tags$b("Font size: Corr text")),
min = 1, max = 30, value = 5, step = 1
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_multi_scatter")
)
)
# column(width = 1) ## empty column
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Corr heatbox panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "CorrHeatBox", value = "corr_heatbox_panel", id = "corr_heatbox_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## corr heat box : select plot variables
shinyWidgets::pickerInput(
inputId = "corr_heatbox_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## corr heat box : select gene groups
gene_group_selection_ui("corr_heat_box_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_corr_heatbox" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
conditionalPanel(
condition = "input.generate_corr_heatbox && output.corr_heatbox_status == true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty column
column(
width = 8,
plotOutput(outputId = "corr_heatbox", height = "auto", width = "auto")
),
column(width = 2) ## empty column
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## corr_heatbox advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
column(
width = 12,
## corr_heatbox labels and Titles
column(
width = 6,
plot_title_and_axis_label_ui(id = "corr_heatbox_title_and_labels")
),
## corr_heatbox Advance options
column(
width = 3,
dropdownButton(
inputId = "corr_heatbox_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = F,
sliderInput(inputId = "corr_heatbox_colors" ,
label = "Number of colors" ,
value = 5,min = 1,
max = 5,
step = 1,
width = "100%"),
hr(),
## Cluster by correlation
shinyWidgets::radioGroupButtons(inputId = "cluster_heatbox" ,
label = tags$h4(tags$b("Cluster variables")),
choices = c("TRUE" = TRUE , "FALSE" = FALSE),
selected = TRUE,
width = "100%",
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success" ,
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## heatbox method
shinyWidgets::radioGroupButtons(inputId = "heatbox_method" ,
label = tags$h4(tags$b("Method")),
choices = c("Circle" ="circle" ,
"Square" = "square") ,
selected = "square",
width = "100%",
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success",
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## heatbox type
shinyWidgets::radioGroupButtons(inputId = "heatbox_type" ,
label = tags$h4(tags$b("Type")),
choices = c("Full" ="full" , "Upper" = "upper" , "Lower" = "lower"),
width = "100%",
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success",
size = "sm" ,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
conditionalPanel(
condition = "input.heatbox_type != 'full'",
## show diagonal
shinyWidgets::radioGroupButtons(inputId = "heatbox_show_diag" ,
label = tags$h4(tags$b("Show diagonal")),
choices = c("TRUE" = TRUE , "FALSE" = FALSE),
selected = "TRUE",
width = "100%" ,
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success" ,
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
hr(),
## corr heatbox scale choice
shinyWidgets::radioGroupButtons(inputId = "corr_heatbox_scale_manual" ,
label = tags$h4(tags$b("Scale")) ,
choices = c("Auto" = "auto" , "Manual" = "manual") ,
selected = "auto" ,
width = "100%" ,
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success",
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## corr heat box manual color scale
conditionalPanel(condition = "input.corr_heatbox_scale_manual == 'manual'" ,
fluidRow(
column(
width = 6,
numericInput(inputId = "corr_heatbox_scale_manual_min" ,
label = "Scale low",
value = -1, min = -1, max = 1,step = 0.1,width = "100%")
),
column(width = 6,
numericInput(inputId = "corr_heatbox_scale_manual_max" ,
label = "Scale high",
value = 1,
min = -1,
max = 1,
step = 0.1,width = "100%")
)
)
),
hr(),
## show / hide corr value
shinyWidgets::radioGroupButtons(
inputId = "heatbox_show_corr_value" ,
label = tags$h4(tags$b("Show corr value")),
choices = c("TRUE"= TRUE, "FALSE" = FALSE),
selected = FALSE ,
width = "100%",
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success",
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
# checkboxInput(inputId = "heatbox_show_corr_value" ,
# label = "Show corr value",value = FALSE , width = "100%"),
hr(),
## corr text font size
sliderInput(
inputId = "heatbox_corr_text_text_size",
label = "Font size: Corr text",width = "100%",
min = 1, max = 30, value = 5, step = 0.1
),
hr(),
## corr text color
colourpicker::colourInput(
inputId = "heatbox_corr_text_col",
label = "Corr text color",
value = "yellow",
returnName = TRUE
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_corr_heatbox")
)
)
# column(width = 1) ## empty column
)
)
)
),
## show corr heatbox data
conditionalPanel(condition = "input.generate_corr_heatbox && output.corr_heatbox_status == true",
shinyBS::bsCollapse(
open = "CorrHeatboxData",
shinyBS::bsCollapsePanel(
title = "CorrHeatboxData",
style = "primary",
DT::dataTableOutput(outputId = "corr_heatbox_data", width = "auto") %>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## density plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Density plot", value = "density_plot_panel", id = "density_plot_panel",
br(),
## select x variables
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select density plot variables
shinyWidgets::pickerInput(
inputId = "density_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## density gene group selection
gene_group_selection_ui("density_plot_gene_group_selection"),
## plot action
hr(),
column(width =6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_density" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display density plot
conditionalPanel(
condition = "input.generate_density && output.density_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty col
## plot output column
column(
width = 8,
plotOutput(outputId = "density_plot", height = "auto")
),
column(width = 2) ## empty col
),
## density plot advanced setting buttons
fluidRow(
hr(),
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "decorate_density_plot")
),
column(
width = 3,
dropdownButton(
inputId = "density_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
## fill and facet density plot
ggplot_fill_and_facet_ui(id = "density_plot_fill_and_facet"),
## density transparency
sliderInput(
inputId = "density_plot_alpha",
label = tags$h4(tags$b("Transparency")), min = 0, max = 1, value = 0.5, step = 0.01, width = "99%"
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_density")
)
)
)
)
)
)
),
## density plot tab panel ends
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## histogram ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Histogram", value = "histogram_panel", id = "histogram_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select histogram variables
shinyWidgets::pickerInput(
inputId = "histogram_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
`live-search` = TRUE,
style = "btn-success"
)
),
gene_group_selection_ui("histogram_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_histogram" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display histogram
conditionalPanel(
condition = "input.generate_histogram && output.histogram_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty col
## plot output column
column(
width = 8,
plotOutput(outputId = "histogram", height = "auto")
),
column(width = 2) ## empty col
),
## histogram advanced options
fluidRow(
hr(),
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "decorate_histogram")
),
column(
width = 3,
dropdownButton(
inputId = "histogram_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
ggplot_fill_and_facet_ui(id = "histogram_fill_and_facet"),
## hitogram position choices.
selectInput(
inputId = "histogram_positions",choices = c("Dodge" = "dodge" , "Stack" = "stack" , "Identity" = "identity"),
label = tags$h4(tags$b("Bar positions")) ,
selected = "dodge",multiple = FALSE, width = "100%"
),
hr(),
## histogram number of bins
numericInput(
inputId = "histogram_number_of_bins",
label = tags$h4(tags$b("Number of bins")), value = 30 , min = 1, max = 1000 , step = 1,
width = "100%"
),
hr(),
## histogram Transparency
sliderInput(
inputId = "histogram_alpha",
label = tags$h4(tags$b("Transparency")), min = 0, max = 1, value = 0.5, step = 0.01 , width = "99%"
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_histogram")
)
)
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Joy plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Joy plot", value = "joy_plot_panel", id = "joy_plot_panel",
br(),
## select x variables
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select joy plot variables
shinyWidgets::pickerInput(
inputId = "joy_plot_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## joy plot gene groups
gene_group_selection_ui("joy_plot_gene_group_selection"),
## plot action
hr(),
column(width =6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_joy_plot" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display Joy plot
conditionalPanel(
condition = "input.generate_joy_plot && output.joy_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty col
## plot output column
column(
width = 8,
plotOutput(outputId = "joy_plot", height = "auto")
),
column(width = 2) ## empty col
),
## joy plot settings
fluidRow(
hr(),
## joy plot labels and title
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui("decorate_joy_plot")
),
## joy plot advance settings
column(
width = 3,
dropdownButton(
inputId = "joy_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,width = "450px",
br(),
## joyplot fill and facet UI
joy_plot_fill_and_facet_ui("joy_plot_fill_and_facet")
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_joy_plot")
)
)
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## box plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Box plot", value = "box_plot_panel", id = "box_plot_panel",
br(),
## select plot varibale
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select x variable
shinyWidgets::pickerInput(
inputId = "box_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success" , `live-search` = TRUE
)
),
gene_group_selection_ui("box_plot_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_box" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display box plot
conditionalPanel(
condition = "input.generate_box && output.box_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty cols
## display box plot
column(
width = 8,
plotOutput(outputId = "box_plot", height = "auto", width = "auto")
),
column(width = 2) ## empty cols
),
## box plot setting options.
fluidRow(
hr(),
column(width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "box_plot_label_and_title")
),
## box plot advance options.
column(
width = 3,
dropdownButton(
inputId = "box_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
## fill and facet ui
ggplot_fill_and_facet_ui(id = "box_plot_fill_and_facet"),
## pvalue
radioGroupButtons(
inputId = "box_plot_pvalue",
label = tags$h4(tags$b("P-value")) ,
size = "sm" , individual = T,
justified = T,
status = "success",
choices = c("Hide" = "FALSE", "Show" = "TRUE"),
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## pvalue method
conditionalPanel(
condition = "input.box_plot_pvalue == 'TRUE'",
selectInput(
inputId = "box_plot_pval_method",
label = tags$h4(tags$b("Method")),
choices = c("t.test" = "t.test", "wilcox.test" = "wilcox.test")
)
),
hr(),
## box plot dots
radioGroupButtons(
inputId = "box_plot_show_dots",
label = tags$h4(tags$b("Dots")) ,
size = "sm" , individual = T,
justified = T,
status = "success",
choices = c("Hide" = "FALSE", "Show" = "TRUE"),
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## box plot dots related UI
conditionalPanel("input.box_plot_show_dots =='TRUE'",
##box plot dots width
sliderInput(inputId = "boxplot_dots_width" ,
label = tags$h4(tags$b("Dots width")),
min = 0.1,
max = 1,
value = 0.1,
step = 0.01,width = "99%"
),
## box plot dots color
colourpicker::colourInput(
inputId = "boxplot_dots_color",
label = tags$h4(tags$b("Dots color")),
value = "black",
returnName = TRUE
),
## box plot dots transparency
sliderInput(inputId = "boxplot_dots_transprancy" ,
label = tags$h4(tags$b("Dots transparency")),
min = 0.1,
max = 1,
value = 0.5,
step = 0.01,
width = "99%"
)
),
## Box transparacny
sliderInput(
inputId = "box_plot_alpha",
label = tags$h4(tags$b("Box transparency")) ,
min = 0,
max = 1,
value = 0.5,
step = 0.01,
width = "99%"
),
hr()
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_box_plot")
)
))
)
)
)
),
## box plot tab panel ends
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## violin plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Violin plot", value = "violin_plot_panel", id = "violin_plot_panel",
br(),
## select plot varibale
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select x variable
shinyWidgets::pickerInput(
inputId = "violin_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## violin plot gene group selection
gene_group_selection_ui("violin_plot_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_violin" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display violin plot
conditionalPanel(
condition = "input.generate_violin && output.violin_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty cols
## display violin plot
column(
width = 8,
plotOutput(outputId = "violin_plot", height = "auto", width = "auto")
),
column(width = 2) ## empty cols
),
## violin plot setting options.
fluidRow(
hr(),
column(width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "violin_plot_label_and_title")
),
## violin plot advance options.
column(
width = 3,
dropdownButton(
inputId = "violin_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
# # fill violin
# shinyWidgets::radioGroupButtons(
# inputId = "fill_violin_plot",
# label = tags$h4(tags$b("Fill by")),
# choices = c("Samples" = "samples", "Sample groups" = "groups" ,
# "Identical" = "identical") ,
# selected = "samples" ,status = "success" ,size = "sm",
# direction = "horizontal",
# individual = TRUE ,
# justified = T,
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
#
# ## fill violin manually
# conditionalPanel(
# condition = "input.fill_violin_plot == 'identical'",
# fluidRow(
# column(
# width = 4,
# colourpicker::colourInput(
# inputId = "violin_plot_color_chooser",
# label = tags$h4(tags$b("Select")) ,
# value = "black",
# returnName = TRUE,
# palette = "limited"
# )
# )
# )
# ),
#
# hr(),
ggplot_fill_and_facet_ui(id = "violin_plot_fill_and_facet"),
# ## pvalue
radioGroupButtons(
inputId = "violin_plot_pvalue",
label = "P-value",
size = "sm" ,
individual = T, justified = T,
status = "success",
choices = c("Hide" = "FALSE", "Show" = "TRUE"),
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## pvalue method
conditionalPanel(
condition = "input.violin_plot_pvalue == 'TRUE'",
selectInput(
inputId = "violin_plot_pval_method",
label = "Method",
choices = c("t.test" = "t.test", "wilcox.test" = "wilcox.test")
)
),
hr(),
## show quantiles lines
shinyWidgets::checkboxGroupButtons(inputId = "violin_show_quantile" ,
label = tags$h4(tags$b("Show quantile")) ,
choices = c("0.1"=0.1, "0.25"=0.35, "0.5"=0.5 , "0.75"=0.75 , "0.9"=0.9) ,
width = "100%",
selected = 0.5 ,
status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T
),
hr(),
# ## flip violin
# shinyWidgets::radioGroupButtons(
# inputId = "violin_flip_xy",
# label = h4(tags$b("Flip axis")),
# choices = c("TRUE" = TRUE, "FALSE" = FALSE),
# selected = "FALSE" , status = "success" ,size = "sm",
# direction = "horizontal",
# individual = TRUE ,
# justified = T,
# width = "300px",
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
# hr(),
# ## facetting
# shinyWidgets::radioGroupButtons(
# inputId = "violin_facet_groups",
# label = h4(tags$b("Separate groups")),
# choices = c("TRUE" = TRUE, "FALSE" = FALSE),
# selected = "FALSE" , status = "success" ,size = "sm",
# direction = "horizontal",
# individual = TRUE ,
# justified = T,
# width = "300px",
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
# hr(),
#
## alpha
sliderInput(
inputId = "violin_plot_alpha",
label = tags$h4(tags$b("Transparency")),
min = 0,
max = 1, value = 0.5, step = 0.01, width = "99%"
),
hr()
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_violin_plot")
)
))
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## bar plot panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Bar plot", value = "barplot_panel", id = "barplot_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
shinyWidgets::pickerInput(
inputId = "barplot_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## select genes to include in the bar plot.
shinyWidgets::pickerInput(
inputId = "barplot_select_genes",
label = "Select genes(s)",
choices = NULL,
choicesOpt = F,
selected = "",
multiple = T,
width = "100%",
options = list(
size = 10,
`selected-text-format` = "count > 10",
`live-search` = TRUE,
style = "btn-success"
)
),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_barplot" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
conditionalPanel(
condition = "input.generate_barplot && output.barplot_status == true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty column
column(
width = 8,
plotOutput(outputId = "barplot", height = "auto", width = "auto")
),
column(width = 2) ## empty column
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## bar plot advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
hr(),
column(width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "barplot_label_and_title")
),
##
column(
width = 3,
dropdownButton(
inputId = "barplot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
## xaxis : genes, or sample
shinyWidgets::radioGroupButtons(
inputId = "barplot_xaxis_choices",
label = h4(tags$b("X-axis")),
choices = c("Genes" = "GeneNames" ,"Samples" = "samples") ,
selected = "GeneNames" ,status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,
width = "400px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon")),
),
hr(),
# bar plot fill bars
shinyWidgets::radioGroupButtons(
inputId = "fill_barplot",
label = h4(tags$b("Fill by")),
choices = c("Manual" = "identical",
"Genes" = "GeneNames" ,"Samples" = "samples",
"Sample groups" = "groups") ,
selected = "samples" ,status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,
width = "400px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## fill bars manually
conditionalPanel(
condition = "input.fill_barplot == 'identical'",
fluidRow(
column(
width = 4,
colourpicker::colourInput(
inputId = "barplot_color_chooser",
label = h4(tags$b("Select")),
value = "black",
returnName = TRUE
)
)
)
),
hr(),
## facetting
shinyWidgets::radioGroupButtons(
inputId = "barplot_facet_value",
label = h4(tags$b("Separate by")),
choices = c("None" = "none" ,
"Genes" = "GeneNames" ,
"Samples" = "samples",
"Sample groups" = "groups"),
selected = "none",status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,
width = "400px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## Y scale during facetting
shinyWidgets::radioGroupButtons(
inputId = "barplot_yscale",
label = h4(tags$b("Scale")),
choices = c("Fix" = "fixed" , "Free" = "free",
"Free X" = "free_x" , "Free Y" = "free_y"),
selected = "fixed",status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,width = "400px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## alpha
sliderInput(
inputId = "barplot_alpha",
label = h4(tags$b("Transparency")),
min = 0,
max = 1,
value = 0.5, step = 0.01, width = "99%"
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_barplot")
)
)
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## PCA plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "PCA plot", value = "pca_plot_panel", id = "pca_plot_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
# PCA plot select variables
shinyWidgets::pickerInput(
inputId = "pca_plot_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE ,
selectOnTab = TRUE
)
),
gene_group_selection_ui("pca_plot_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_pca_plot" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
conditionalPanel(
condition = "input.generate_pca_plot && output.pca_plot_status == true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
#column(width = 2), ## empty column
column(
width = 9,
plotOutput(outputId = "pca_plot",
brush = "pca_plot_brush",
height = "auto",
width = "auto") #%>% shinycssloaders::withSpinner(color = "#18BC9C")
),
### show / hide sample groups
column(width = 3 ,
shinyWidgets::multiInput(width = "100%",
inputId = "pca_plot_hide_sample_groups",
label = "Show / Hide sample groups",
choices = "") %>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## PCA plot advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
hr(),
# column(width = 1), ## empty column
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "decorate_pca_plot")
),
column(
width = 3,
## PCA Advance options drop down menu.
dropdownButton(
inputId = "pca_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
## select PCs
shiny::selectizeInput("select_pcs_to_plot", label="Select PCs",
choices=NULL,
multiple=TRUE ,
options = list(maxItems = 2)),
## display / hide sample names
shinyWidgets::radioGroupButtons(inputId = "pca_display_sample_names",
label = tags$h4(tags$b("Disply sample names")) ,
choices = c("TRUE" = TRUE, "FALSE" = FALSE),
selected = "FALSE",status = "success" ,
size = "sm",
direction = "horizontal", individual = TRUE ,
justified = T,
width = "300px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## PCA sample names size .
conditionalPanel(condition = "input.pca_display_sample_names == 'TRUE'" ,
sliderInput(
inputId = "pca_plot_sample_names_size",
label = tags$h4(tags$b("Font size: Sample names")),
min = 1,
max = 10,
value = 5,
step = 0.05
),
hr()
),
## PCA dot size.
sliderInput(inputId = "pca_sample_dot_size" ,
label = tags$h4(tags$b("Dot size")),
min = 1,
max = 10,
value = 5,
step = 0.05),
hr(),
## pca colors
shinyWidgets::radioGroupButtons(inputId = "pca_plot_colour" ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
label = tags$h4(tags$b("Color by")) ,
choices = c("Identical"="identical",
"Sample groups" = "groups" ,
"K-means" = "kmeans") ,
selected = "identical" ,
width = "300px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## color choices color identical
conditionalPanel(condition = "input.pca_plot_colour == 'identical' " ,
colourpicker::colourInput(
inputId = "pca_sample_name_color",
label = tags$h4(tags$b("Select color")),
value = "black",
returnName = TRUE
)
),
## color choices color identical
conditionalPanel(condition = "input.pca_plot_colour == 'kmeans' " ,
shiny::numericInput(inputId = "pca_sample_sample_kmeans_n" ,
label = "Number of cluster" ,
value = 1 , step = 1, min = 1, max = 100)
)
)
),
## export plot as imagess
column(
width = 3,
export_plot_ui(id = "export_pca_plot")
)
)
)
)
),
### Triggered actions
## set axis and plot titles
shinyBS::bsModal(
id = "pca_plot_edit_titles", title = "Title and labels", trigger = "trigger_pca_plot_edit_titles",
## plot titles
h4(tags$b("Title")),
textInputIcon(inputId = "pca_plot_title",
label = "",
value = "",
placeholder = "Main :"),
hr()
)
),
### pca plot brushed points datatable
fluidRow(
column(width = 12,
conditionalPanel(
condition = "output.pac_plot_brushed_data_table_status==true",
shinyBS::bsCollapse(
open = "Selected SRA points sample information (Does not apply to user uploaded data)",
shinyBS::bsCollapsePanel(
title = "Selected SRA points sample information (Does not apply to user uploaded data)", style = "primary",
DT::dataTableOutput(outputId = "pca_brushed_datatable", width = "auto") %>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## line plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Line plot", value = "line_plot_panel", id = "line_plot_panel",
br(),
## select plot varibale
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select x variable
shinyWidgets::pickerInput(
inputId = "lineplot_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## select line plot gene groups
gene_group_selection_ui(id = "line_plot_gene_group_selection"),
hr(),
fluidRow(
column(width = 12,
## line plot gene selection
shinyWidgets::radioGroupButtons(
inputId = "lineplot_genes_selection",
label = tags$h4(tags$b("Genes to plot")),
choices = c("# top variable genes (By standard deviation)" = "top_variable_genes", "All genes" = "all"),
individual = T,
justified = T,
status = "success" ,
size = "sm" ,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## number of top variable genes for lineplot
conditionalPanel(
condition = "input.lineplot_genes_selection == 'top_variable_genes'",
numericInput(
inputId = "lineplot_top_n_genes",
label = tags$h4(tags$b("# top variable genes to show")),
value = 500, min = 50, max = 2000, step = 50 #width = "100%"
)
),
hr(),
## line plot clustering
shinyWidgets::radioGroupButtons(
inputId = "line_plot_cluster_genes_by",
label = tags$h4(tags$b("Gene cluster")),
choices = c("K-means" = "kmeans",
"Gene groups" = "gene_groups"),
individual = T,
justified = T,
status = "success" ,
size = "sm" ,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## line plot number of k-means cluster
conditionalPanel(
condition = "input.line_plot_cluster_genes_by == 'kmeans'",
numericInput(
inputId = "line_plot_nclust",
label = tags$h4(tags$b("# of clusters (k-means)")),
value = 5, min = 1, max = 10, step = 1
)
),
hr(),
## line plot choice for value to use in cluster
fluidRow(
column(
width = 6,
shinyWidgets::radioGroupButtons(
inputId = "lineplot_cluster_value_type",
label = tags$h4(tags$b("Cluster by")),
choices = c("Raw value" = "raw_val" ,
"Z-Score" = "zscore"),
selected = "zscore", justified = T,
size = "sm" ,
status = "success",
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
## line plot choice of value to display
column(
width = 6,
shinyWidgets::radioGroupButtons(
inputId = "lineplot_display_value_type",
label = tags$h4(tags$b("Display value")),
choices = c("Raw value" = "raw" , "Z-Score" = "zscore"),
selected = "zscore",
size = "sm" ,
justified = T,
status = "success",
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
)
),
hr(),
## all lines or average line
shinyWidgets::radioGroupButtons(inputId = "activate_avg_line_plot" ,
label = tags$h4(tags$b("Display lines for")) ,
choices = c("Individual gene" = "individual" , "Average of all"= "average" ) ,
selected = "individual",
size = "sm" ,
width = "100%" ,
justified = T,
individual = T,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon")),
status = "success"),
## average line type : mean or median
conditionalPanel(
"input.activate_avg_line_plot == 'average'",
shinyWidgets::radioGroupButtons(inputId = "avg_line_type" ,
label = "Average type" ,
choices = c("Mean" = "mean",
"Median" = "median") ,
selected = "median",
size = "sm" ,
width = "100%" ,
justified = T,
individual = T,
status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
)
)
),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_lineplot" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## line plot plot panel
conditionalPanel(
condition = "input.generate_lineplot && output.line_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 1), ## empty column
## display line plot
column(
width = 10, #style = "overflow-y:auto;",
plotOutput(outputId = "line_plot",
height = "auto",
width = "auto")),
column(width = 1) ## empty column
),
## line plot advance options
fluidRow(
hr(),
## line plot title and labels
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "decorate_line_plot")
),
## line plot Advance options
column(
width = 3,
dropdownButton(
inputId = "line_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
## line plot color choices
shinyWidgets::radioGroupButtons(
inputId = "line_plot_color_by",
label = tags$h4(tags$b("Color")),
choices = rlang::set_names(c("gene_groups","identical") ,
c("Gene groups", "Identical")),
individual = T,
justified = T,
status = "success" ,
size = "sm" ,
width = "300px"
),
## line plot color indentical
conditionalPanel(
condition = paste0("input.line_plot_color_by == 'identical'"),
fluidRow(
column(
width = 4,
colourpicker::colourInput(
inputId = "line_plot_color_chooser",
label = tags$h4(tags$b("Select")),
value = "black",
returnName = TRUE
)
)
)
),
hr(),
## line plot facet
shinyWidgets::radioGroupButtons(
inputId = "line_plot_separate_by",
label = tags$h4(tags$b("Separate by")),
choices = rlang::set_names(c("none" , "gene_groups") ,
c("None" , "Gene groups")),
individual = T,
justified = T,
status = "success" ,
size = "sm" ,
width = "300px"
),
hr(),
## scale y
conditionalPanel("input.line_plot_separate_by == 'gene_groups'",
shinyWidgets::radioGroupButtons(inputId = "line_plot_facet_scale_free",
label = "Scales" ,
choices = c("Fix" ="fixed" ,
"Free" = "free",
"Free X" ="free_x",
"Free Y" = "free_y"),
selected = "fixed" ,
status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr()
),
hr(),
## line plot splin shape
sliderInput(inputId = "line_plot_splin_shape" ,
label = tags$h4(tags$b("Line shape")) ,
min = -1,
max = 1,
step = 0.01 ,
value = 0 ,
width = "99%"),
hr(),
## line plot line transparency
sliderInput(inputId = "line_plot_line_transparancy" ,
label = tags$h4(tags$b("Transparency")) ,
min = 0,
max = 1,
step = 0.01 ,
value = 0.5 ,
width = "99%"),
hr(),
## fix number of columns in the facetted ggplot.
numericInput(inputId = "line_plot_ncols",
label = tags$h4(tags$b("Number of columns")),
value = 3 ,
min = 1,
max = 10,
step = 1,
width = "100%"),
hr(),
## line plot point size
sliderInput(inputId = "lineplot_point_size" ,
label = "Point size" ,
min = 1,
max = 10,
value = 2,
step = 0.01),
## line plot line size
sliderInput(inputId = "lineplot_line_size" ,
label = "Line size" ,
min = 1,
max = 10,
value = 2,
step = 0.01)
)
),
## line plot export
column(
width = 3,
export_plot_ui(id = "export_line_plot")
)
)
)
)
),
## line plot data or functional analysis
radioGroupButtons(
inputId = "lineplot_data_or_functional_analysis",
choices = c("Show Data" = "show_lineplot_data",
"Functional Analysis" = "lineplot_functional_analysis"),
status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon")) ,
size = "normal" ,
direction = "horizontal" ,
justified = TRUE , individual = TRUE ,
width = "100%",
selected = ""
),
br(),
## show lineplot data
conditionalPanel(
condition = "input.lineplot_data_or_functional_analysis == 'show_lineplot_data'",
shinyBS::bsCollapse(
open = "Clustered data",
shinyBS::bsCollapsePanel(
title = "Clustered data", style = "primary",
DT::dataTableOutput(outputId = "line_plot_clustred_data", width = "auto") %>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
)
),
## show lineplot functional analysis
conditionalPanel(
condition = "input.lineplot_data_or_functional_analysis == 'lineplot_functional_analysis'",
shinyBS::bsCollapse(
open = "Functional analysis",
shinyBS::bsCollapsePanel(
title = "Functional analysis", style = "primary",
functional_analysis_ui(id = "lineplot_functional_analysis_ui")
)
)
)
),
## triggered action
shinyBS::bsModal(
id = "line_edit_titles", title = "Edit titles", trigger = "trigger_line_edit_titles",
## plot titles
textInput(inputId = "line_plot_title", label = "Plot Title", value = ""),
hr(),
textInput(inputId = "line_x_axis_title", label = "Axis title: X", value = ""),
hr(),
textInput(inputId = "line_y_axis_title", label = "Axis title: Y", value = "value")
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Heatmap tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Heatmap", value = "heatmap_panel", id = "heatmap_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
column(
width = 12, #style = "overflow-x:auto;",
## select heatmap variables
shinyWidgets::pickerInput(
inputId = "heatmap_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## heatmap select gene groups
gene_group_selection_ui(id = "heatmap_select_gene_groups"),
hr(),
## top variable genes to plot in heatmap
shinyWidgets::radioGroupButtons(
inputId = "hm_genes_selection",
label = tags$h4(tags$b("Number of genes to plot")),
choices = c("# top variable genes (By standard deviation)" = "top_variable_genes", "All genes" = "all"),
selected = "top_variable_genes" ,
status = "success" ,
size = "normal",
direction = "horizontal",
justified = T, individual = T ,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
conditionalPanel(
condition = "input.hm_genes_selection == 'top_variable_genes'",
# heatmap top n genes
numericInput(
inputId = "heatmap_top_n_genes",
label = tags$h4(tags$b("# top variable genes to show")),
value = 500, min = 50, max = 2000, step = 50 #width = "25%"
)
),
hr(),
## heatmap choice for value to use in cluster
fluidRow(
column(
width = 6,
shinyWidgets::radioGroupButtons(
inputId = "heatmap_cluster_value_type",
label = tags$h4(tags$b("Cluster by")),
choices = c("Raw value" = "raw_val" , "Z-Score" = "zscore"),
selected = "zscore",status = "success",
size = "normal",
direction = "horizontal" ,
justified = T , individual = T, width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
## heatmap choice of value to plot
column(
width = 6,
shinyWidgets::radioGroupButtons(
inputId = "heatmap_display_value_type",
label = tags$h4(tags$b("Display value")),
choices = c("Raw value" = "raw" , "Z-Score" = "zscore"),
selected = "zscore",
direction = "horizontal" ,
justified = T ,
individual = T,
width = "100%" , status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
)
),
hr(),
# heat map column row and legend options
fluidRow(
#style = "min-width:1200px",
style = "overflow-x:auto;",
column(
width = 4, style = "min-width:150px",
# heatmap row options
shinyBS::bsCollapse(
open = "Row options",
shinyBS::bsCollapsePanel(
title = "Row options", style = "primary",
## Row names"
shinyWidgets::radioGroupButtons(
inputId = "show_hm_row_names",
label = tags$h4(tags$b("Row names")),
choices = c("TRUE" = TRUE, "FALSE" = FALSE),
selected = FALSE , status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## Font size : Row names
sliderInput(
width = "100%",
inputId = "hm_row_names_font_size",
label = tags$h4(tags$b("Row names font size")),
min = 0.1,
max = 20,
value = 5,
step = 0.1
),
## Adjust height : Rows
# sliderInput(
# width = "100%",
# inputId = "hm_row_height",
# label = tags$h4(tags$b("Row height")),
# min = 0.1,
# max = 50,
# value = 0.1,
# step = 0.1
# ),
## Row clusters
shinyWidgets::radioGroupButtons(
inputId = "heatmap_row_clusters_choices" ,
label = tags$h4(tags$b("Row cluster")),
choices = c("K-means" = "kmeans" , "Gene groups" ="gene_groups"),
selected = "kmeans",
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## of clusters (k-means)
conditionalPanel(condition = "input.heatmap_row_clusters_choices == 'kmeans'",
numericInput(
width = "100%",
inputId = "heatmap_row_nclust",
label = tags$h4(tags$b("# of row clusters (k-means)")),
value = 1,
min = 1,
max = 10,
step = 1
)
),
## row cluster prefix
shiny::textInput(inputId = "hm_cluster_prefix" ,
label = tags$h4(tags$b("Row cluster label prefix")) , value = "Clust_" ,
width = "100%" , placeholder = "Text will appear as row cluster name prefix" ),
# Cluster rows (within the cluster)
shinyWidgets::radioGroupButtons(
inputId = "hm_cluster_rows",
label = tags$h4(tags$b("Row cluster (within the cluster)")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
# # Cluster row slices
# shinyWidgets::radioGroupButtons(
# inputId = "hm_cluster_row_slice",
# label = tags$h4(tags$b("Arrange row cluster slice")),
# choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
# selected = TRUE ,
# status = "success",
# size = "sm",
# direction = "horizontal",
# justified = T,
# individual = T,
# width = "100%",
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
#
## show / hide row dendogram
conditionalPanel(
condition = "input.hm_cluster_rows == 'TRUE'",
shinyWidgets::radioGroupButtons(
inputId = "show_hm_row_dend",
label = tags$h4(tags$b("Row dendogram")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
# show border around cluster
shinyWidgets::radioGroupButtons(
inputId = "hm_border",
label = tags$h4(tags$b("Row cluster border")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## std dev heatmap
shinyWidgets::radioGroupButtons(
inputId = "show_std_dev_hm",
label = tags$h4(tags$b("Add standard deviation heatmap")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## sort by SD heatmap
conditionalPanel(condition = "input.show_std_dev_hm == 'TRUE'" ,
shinyWidgets::radioGroupButtons(
inputId = "sort_hm_by_std_dev",
label = tags$h4(tags$b("Sort by standard deviation")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
)
)
)
),
column(
width = 4, style = "min-width:150px;",
## heatmap column options
shinyBS::bsCollapse(
open = "Column options",
shinyBS::bsCollapsePanel("Column options",
style = "primary",
## heatmap show / hide column names
shinyWidgets::radioGroupButtons(
inputId = "show_hm_colum_names",
label = tags$h4(tags$b("Column names")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = TRUE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## heatmap change font size column names
sliderInput(
inputId = "hm_column_names_font_size",
label = tags$h4(tags$b("Column names font size")),
min = 0.1,
max = 20,
value = 10,
step = 0.1,
width = "100%"
),
# ## adjust column width
# sliderInput(
# inputId = "hm_col_width",
# label = tags$h4(tags$b("Column width")),
# min = 0.1,
# max = 50,
# value = 0.5,
# step = 0.1,
# width = "100%"
# ),
## Column clusters
shinyWidgets::radioGroupButtons(
inputId = "heatmap_column_clusters_choices" ,
label = tags$h4(tags$b("Column cluster")),
choices = c("K-means" = "kmeans" , "Sample groups" ="sample_groups"),
selected = "kmeans",
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## number of column cluster
conditionalPanel(
condition = "input.heatmap_column_clusters_choices == 'kmeans'",
numericInput(
width = "100%",
inputId = "heatmap_coulm_nclust",
label = tags$h4(tags$b("# of column clusters (k-means)")),
value = 1,
min = 1,
max = 10,
step = 1
)
),
## column cluster prefix
shiny::textInput(inputId = "hm_column_cluster_prefix" ,
label = tags$h4(tags$b("Column cluster label prefix")) , value = "Clust_" ,
width = "100%" , placeholder = "Text will appear as column cluster name prefix" ),
## heatmap cluster column with in the cluster
shinyWidgets::radioGroupButtons(
inputId = "hm_cluster_columns",
label = tags$h4(tags$b("Column cluster (within the cluster)")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
# # Cluster column slices
# shinyWidgets::radioGroupButtons(
# inputId = "hm_cluster_column_slice",
# label = tags$h4(tags$b("Arrange column cluster slice")),
# choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
# selected = TRUE ,
# status = "success",
# size = "sm",
# direction = "horizontal",
# justified = T,
# individual = T,
# width = "100%",
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
#
## show / hide column dendogram
conditionalPanel("input.hm_cluster_columns == 'TRUE'",
shinyWidgets::radioGroupButtons(
inputId = "show_hm_column_dend",
label = tags$h4(tags$b("Column dendogram")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
## heatmap top annotations
shinyWidgets::checkboxGroupButtons(
inputId = "heatmap_anno_type",
label = tags$h4(tags$b("Column annotation")),
choices = c("Sample groups" = "show_heatmap_column_groups",
"Boxplot" = "show_heatmap_column_boxplot") ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## heatmap top annot height
sliderInput(inputId = "heatmap_top_annot_height" ,
label = tags$h4(tags$b("Column annotaion height")) ,
min = 1 , max = 10,
step = 0.05 , value = 1 , width = "100%")
)
)
),
column(
width = 4, style = "min-width:150px;",
# heatmap legend options
shinyBS::bsCollapse(
open = "Legend options",
shinyBS::bsCollapsePanel("Legend options",
style = "primary",
textInput(inputId = "heatmap_legend_name",
label = tags$h4(tags$b("Legend name")),
value = "Value",
width = "100%"),
## heatmap legend position
radioGroupButtons(
width = "100%",
inputId = "heatmap_legend_pos",
label = tags$h4(tags$b("Legend position")),
individual = T,justified = T,
choices = c("T" = "top", "B" = "bottom", "L" = "left", "R" = "right"),
selected = "right",status = "success" ,
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## heatmap legend direction
radioGroupButtons(
width = "100%",
inputId = "heatmap_legened_direction",
label = tags$h4(tags$b("Legend direction")),
individual = T,justified = T,
choices = c("H" = "horizontal", "V" = "vertical"),
selected = "vertical",
status = "success" , size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
br(),
tags$h4(tags$b(("Heatmap Colors"))),
## heatmap color panel
shiny::wellPanel(
## heatmap color : low
colourpicker::colourInput(
inputId = "heatmap_col_low",
label = tags$h4(tags$b("Low")),
value = "#032E80",
returnName = TRUE
),
## heatmap color : med
colourpicker::colourInput(
inputId = "heatmap_col_medium",
label = tags$h4(tags$b("Middle")),
value = "white",
returnName = TRUE
),
## heatmap color : high
colourpicker::colourInput(
inputId = "heatmap_col_high",
label = tags$h4(tags$b("High")),
value = "#910200",
returnName = TRUE
)
),
### set legend minimum
br(),
tags$h4(tags$b(("Heatmap scale"))),
## heatmap scale
wellPanel(
numericInput(inputId = "heatmap_scale_min" ,
label = tags$h4(tags$b("Minimum")),
value = 0),
### set legend maximum
numericInput(inputId = "heatmap_scale_max" ,
label = tags$h4(tags$b("Maximum")) ,
value = 20 )
)
)
)
)
),
hr(),
## generate heatmap submit button.
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_heatmap" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
)
),
## heatmap plot panel
conditionalPanel(
condition = "input.generate_heatmap && output.heatmap_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(style = "overflow-y:auto; max-height:2000px; position:auto;",
column(width = 1), ## empty column
## display heatmap
column(
width = 11,
shinycssloaders::withSpinner(ui_element = plotOutput(outputId = "heatmap",
height = "auto", width = "auto"),
color = "#18BC9C")
),
column(width = 1) ## empty column
),
hr(),
## empty col
column(width = 1),
column(width = 10,
column(width = 6,
## adjust current heatmap height and width
dropdownButton(
inputId = "plot_hm_drop_down",
icon = icon("resize-full", lib = "glyphicon"),
label = "Heatmap browser dimensions",
size = "sm",
circle = F,
status = "success",
up = T,
right = F,
# Adjust height : Rows
sliderInput(
#width = "100%",
inputId = "hm_row_height",
label = tags$h4(tags$b("Row height")),
min = 0.1,
max = 50,
value = 0.1,
step = 0.1
),
## adjust column width
sliderInput(
inputId = "hm_col_width",
label = tags$h4(tags$b("Column width")),
min = 0.1,
max = 50,
value = 0.5,
step = 0.1,
#width = "100%"
)
)
),
column(width = 6,
## export heatmap
export_base_graphics_ui(id = "export_heatmap")
)
), ## empty column
column(width = 1) ## empty column
)
),
## show / hide heatmap data , perform functional analysis , wordcloud.
radioGroupButtons(
inputId = "heatmap_data_or_functional_analysis",
choices = c("Heatmap all data + gene annotation" = "show_heatmap_data",
"Heatmap clusters" = "show_heatmap_clusters",
"Functional analysis" = "heatmap_functional_analysis" ,
"Sample information" = "display_sample_inforamtion"
),
status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon")) ,
size = "normal" ,
direction = "horizontal" ,justified = TRUE ,
individual = TRUE ,
width = "100%",selected = ""
),
br(),
## display heatmap clusters
conditionalPanel(
condition = "input.heatmap_data_or_functional_analysis == 'show_heatmap_clusters'",
shinyBS::bsCollapse(
open = "Heatmap clusters",
shinyBS::bsCollapsePanel(
title = "Heatmap clusters", style = "primary",
## heatmap cluster side : row or column
div(style="display: inline-block;vertical-align:top; width: 300px;",
shinyWidgets::radioGroupButtons(inputId = "heatmap_cluster_type" ,
label = "Cluster type" ,
choices = c("Row side" = "show_hm_row_side_clusters" ,
"Column side" = "show_hm_column_side_clusters") ,
checkIcon = list(yes = icon("ok",
lib = "glyphicon")),
selected = "show_hm_row_side_clusters" ,
status = "success" ,size = "normal" ,
direction = "horizontal" ,individual = T)
),
## heatmap cluster format : wide or long
div(style="display: inline-block;vertical-align:top; width: 300px;",
shinyWidgets::radioGroupButtons(inputId = "heatmap_cluster_data_format" ,
label = "Data format" ,
choices = c("Wide" = "wide" ,
"Long" = "long") ,
checkIcon = list(yes = icon("ok",
lib = "glyphicon")),
selected = "wide" , status = "success" ,size = "normal" ,
direction = "horizontal" ,individual = T)
),
hr(),
## hm cluster data output
shinycssloaders::withSpinner(
ui_element = DT::dataTableOutput(outputId = "heatmap_display_cluster_data",
width = "auto"),
color = "#18BC9C")
)
)
),
## display heatmap expr mat
conditionalPanel(
condition = "input.heatmap_data_or_functional_analysis == 'show_heatmap_data'",
shinyBS::bsCollapse(
open = "Heatmap all data + gene annotation",
shinyBS::bsCollapsePanel(
title = "Heatmap all data + gene annotation", style = "primary",
DT::dataTableOutput(outputId = "heatmap_data", width = "auto")%>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
)
),
## heatmap functional analysis
conditionalPanel(
condition = "input.heatmap_data_or_functional_analysis == 'heatmap_functional_analysis'",
shinyBS::bsCollapse(
open = "Functional analysis",
shinyBS::bsCollapsePanel(
title = "Functional analysis", style = "primary",
functional_analysis_ui(id = "heatmap_functional_analysis_ui")
)
)
),
## heatmap sample information
conditionalPanel(condition = "input.heatmap_data_or_functional_analysis == 'display_sample_inforamtion' " ,
shinyBS::bsCollapse(
open = "Sample information",
shinyBS::bsCollapsePanel(
title = "Sample information", style = "primary",
fluidRow(
column(
width = 12,
cluster_wise_sample_information_ui("hm_sample_infor")
)
)
)
)
)
)
)
)
)
)
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## About page ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
navbarMenu(title = "About",icon = icon("tag"),
## About page
tabPanel(title = tags$a(icon("searchengin"),
icon = icon("searchengin"),
href = "https://cparsania.github.io/FungiExpresZ/about.html" ,
"Overview",target="_blank")),
# tags$style(HTML("
# section.page-header {
# display: none;
# }
#
# section.main-content{
# max-width: 1000px;
# font-size: 100%;
# }
#
# div#TOC{
# max-width: 1024px;
# font-size: 100%;
# }
# ")),
# includeHTML(system.file("app","rmd_and_html","about.html" , package = "FungiExpresZ"))
# ),
## Video Tutorial page
tabPanel(title = "Video Tutorials", icon = icon("chalkboard-teacher"),
tags$style(HTML("
section.page-header {
display: none;
}
section.main-content{
max-width: 1000px;
font-size: 100%;
}
div#TOC{
max-width: 1024px;
font-size: 100%;
}
")),
includeHTML(system.file("app","rmd_and_html","tutorial.html" , package = "FungiExpresZ"))
),
## Step by step guide page
tabPanel(title = tags$a(icon("paperclip"),
icon = icon("paperclip"),
href = "https://cparsania.github.io/FungiExpresZ/step_by_step_guide.html" ,
"Step-by-step tutorial",target="_blank"))
# tags$style(HTML("
# section.page-header {
# display: none;
# }
#
# section.main-content{
# max-width: 1000px;
# font-size: 100%;
# }
#
# div#TOC{
# max-width: 1024px;
# font-size: 100%;
# }
# ")),
# includeHTML(system.file("app","rmd_and_html","step_by_step_guide.html" , package = "FungiExpresZ"))
# )
#
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Download page ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
navbarMenu(title = "Downloads",
## download GO data
tabPanel("GO data",icon = icon("file-download"),
download_go_data_ui("download_go_data")
),
## download gene expression data
tabPanel("Gene expression data", icon = icon("file-download"),
download_gene_expression_matrix("download_gene_expression_data")
),icon = icon("download") ),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## News & Updates ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(title = "News & Updates", icon = icon("newspaper"),
tags$style(HTML("
section.page-header {
display: none;
}
section.main-content{
max-width: 1000px;
font-size: 100%;
}
div#TOC{
max-width: 1024px;
font-size: 100%;
}
")),
includeHTML(system.file("app","rmd_and_html","newz_and_update.html" , package = "FungiExpresZ"))
#includeHTML("doc/newz_and_update.html")
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Citations page ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(title = "Citations", icon = icon("stack-exchange"),
tags$style(HTML("
section.page-header {
display: none;
}
section.main-content{
max-width: 1000px;
font-size: 100%;
}
div#TOC{
max-width: 1024px;
font-size: 100%;
}
")),
includeHTML(system.file("app","rmd_and_html","citations.html" , package = "FungiExpresZ"))
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## contact page ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
navbarMenu("Contact",
icon = icon("envelope"),
tabPanel(title = tags$a(icon("github"),href = "https://github.com/cparsania/FungiExpresZ" ,
"GitHub",target="_blank")),
tabPanel(title = tags$a(icon("at"), href = "mailto:chirag.parsania@gmail.com",
"Email")),
tabPanel(title = tags$a(icon("twitter"),href = "https://twitter.com/ChiragParsania" ,
"@ChiragParsania",target="_blank"))
)
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## app footer ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
hr(),
tags$style(type='text/css', "#app_footer { text-align: center;}"),
tags$div(id = "app_footer",tags$b("FungiExpresZ"), "is developed by ",
tags$a(tags$b("Chirag Parsania ") , icon("twitter") ,
href= "https://twitter.com/ChiragParsania"), "from ",
tags$a(tags$b("Chris Wong's Lab ") , icon("twitter") , href = "https://twitter.com/ChrisKHWong"), "at University of Macau."),
tags$div(id = "app_footer", "For any query or suggestions, please contact",
tags$a(icon("github"),href = "https://github.com/cparsania/FungiExpresZ" ,
"GitHub",target="_blank"),
tags$a(icon("at"), href = "mailto:chirag.parsania@gmail.com",
"Email"),
"."),
br(),
## display latest release
# tags$div(
# style = "text-align:center;",
#
# ),
br(), br(), br(), br(), br(), br(), br(), br()
)
)
}
#' @import shiny
golem_add_external_resources <- function(){
addResourcePath(
'www', system.file('app/www', package = 'FungiExpresZ')
)
tags$head(
golem::activate_js(),
golem::favicon(ico = "www/favicon.ico" , rel = "shortcut icon"),
golem::favicon(ico = "www/apple-touch-icon.png" , rel = "apple-touch-icon"),
golem::favicon(ico = "www/favicon-32x32.png" , rel = "icon"),
golem::favicon(ico = "www/favicon-16x16.png" , rel = "icon"),
golem::favicon(ico = "www/site.webmanifest" , rel = "manifest"),
tags$script(src="www/google_analytics.js")
#tags$html("www/markdown/Tutorial.html"),
#tags$html("www/markdown/newz_and_update.html")
# Add here all the external resources
# If you have a custom.css in the inst/app/www
# Or for example, you can add shinyalert::useShinyalert() here
#tags$link(rel="stylesheet", type="text/css", href="www/custom.css")
#tags$head(includeScript("www/google_analytics.js"))
)
}
cparsania/FungiExpresZ documentation built on March 15, 2024, 5:48 p.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions golem_add_external_resources app_ui
Documented in app_ui
#' app_ui
#' @import ggplot2
#' @import png
#' @import ggridges
#' @import wordcloud
#' @import clusterProfiler
#' @import shinycssloaders
#' @import ggcorrplot
#' @import prettydoc
#' @import svglite
#' @import circlize
#' @import GGally
#' @import ggfortify
#' @import ggrepel
#' @import ComplexHeatmap
#' @import shinyWidgets
#' @import ggpubr
#' @import shiny
#' @import golem
#' @import htmltools
#' @import processx
#' @import attempt
#' @import shinythemes
#' @import viridis
#' @import formattable
#' @import colourpicker
#' @import ggalt
#' @import gtools
#' @import shinyBS
#' @importFrom scales hue_pal
#' @importFrom shinyjs hide
#' @importFrom shinyjs show
#' @importFrom shinyjs enable
#' @importFrom shinyjs disable
#' @importFrom shinyjs useShinyjs
#' @importFrom DT renderDataTable
#' @importFrom DT dataTableProxy
#' @importFrom DT selectRows
#' @importFrom DT dataTableOutput
#' @importFrom DT JS
#' @importFrom DT datatable
#' @importFrom badger ver_devel
#'
#' @keywords internal
#'
app_ui <- function() {
tagList(
# Leave this function for adding external resources
golem_add_external_resources(),
# List the first level UI elements here
fluidPage(
#tags$head(includeScript("./google_analytics.js")),
#tags$head(includeScript("./inst/app/www/google_analytics.js")),
#tags$head(includeScript("www/google_analytics.js")),
theme = shinythemes::shinytheme("flatly"),
shinyjs::useShinyjs(),
## import google fonts
tags$head(
tags$style(HTML("
@import url('https://fonts.googleapis.com/css?family=Ribeye&display=swap'
"))
),
## arrange title panel
tags$div(
#tags$a(img(src="https://raw.githubusercontent.com/cparsania/FungiExpresZ/master/inst/app/www/hex_sticker.png" , height="150")),
titlePanel(
tags$h1("Fungi",
tags$a(img(src="https://raw.githubusercontent.com/cparsania/FungiExpresZ/master/inst/app/www/hex_sticker.png" , height="100"),
href = "https://raw.githubusercontent.com/cparsania/FungiExpresZ/master/inst/app/www/hex_sticker.png" , target= "_blank"),
"ExpresZ",
tags$h2("Fungal Gene Expression Data Analysis and Visualization Tool" , style = "font-family: 'Ribeye'") ,
align = "center",
style = "font-family: 'Ribeye'; font-size: 80px;"
),
windowTitle = "FungiExpresZ") ,
style = "color:white;
background-color:#2C3E50;
text-align: center;
padding: 5px 0 "),
# CSS reference : https://stackoverflow.com/questions/28630433/how-to-align-navbar-to-center-with-css
## adjust navbar panel
tags$style(HTML("
ul.nav.navbar-nav {
left: 0px;
width: 100%;
display: flex;
justify-content: center;
}")),
#navbar navbar-default navbar-static-top
navbarPage(collapsible = T,fluid = T,
title = "",
tabPanel(title = "App", icon = icon("home"),
sidebarLayout(
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## UI sidebar panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
sidebarPanel(
width = 3,
h2("Inputs"),
## upload data
shinyBS::bsCollapse(
open = c("Select / Upload data" , "Assign Groups"),
multiple = T,
shinyBS::bsCollapsePanel(
title = "Select / Upload data", style = "primary",
radioButtons(inputId = "data_selection",
label = "",
choices = c("Select data" = "select_sample",
"Upload / Use example data" = "upload_user_data"),
inline = F),
## select data action button
conditionalPanel(
condition = "input.data_selection =='select_sample'",
shinyWidgets::actionBttn(
inputId = "select_sample_trigger",
label = "Select", color = "success",
style = "gradient", size = "md",
icon = icon("database"), block = T
)
),
## Select datatrigger
shinyBS::bsModal(
id = "trigger_select_sample_data",
title = fluidRow(
fluidRow(column(11, offset = 1,tags$h2(tags$b("Sequence Read Archive (SRA) Run Inforamation Table"))))
),
trigger = "select_sample_trigger",
size = "large",
## row having selection instruction
fluidRow(
column (
width = 12,
tags$h3(tags$b("Click on row(s) to select SRA samples for analysis and visualisation.", tags$br() , tags$br(), "Once selection made click submit."))
)
),
hr(),
## row having row filter title
fluidRow(
column(
width = 4,
offset = 5,
tags$h2(tags$b("Row filters"))
)
),
### row having filer buttons
fluidRow(
column(
width = 4,
## Species
shinyWidgets::pickerInput(
inputId = "select_species",
selected = "Aspergillus nidulans",
label = "Organism",
choices = NULL,
choicesOpt = T,
width = "100%",
options = list(
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", "max-options" = 1, `live-search` = TRUE
)
)
),
## Strain
column(
width = 4,
shinyWidgets::pickerInput(
inputId = "select_strain",
label = "Strain",
choices = NULL,
choicesOpt = F,
selected = "",
multiple = T,
width = "100%",
options = shinyWidgets::pickerOptions(liveSearch = TRUE,
size = 10 ,
selectedTextFormat = "count > 10" ,
maxOptions = 1,
style = "btn-success")
)
),
## Genotype
column(
width = 4,
shinyWidgets::pickerInput(
inputId = "select_genotype",
label = "Genotype",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = shinyWidgets::pickerOptions(liveSearch = TRUE,
size = 10 ,
selectedTextFormat = "count > 10" ,
maxOptions = 1,
style = "btn-success")
)
)
),
## reset filters
fluidRow(
column(width = 4,
offset = 4,
## reset strain
shinyWidgets::actionBttn(
inputId = "reset_strain_filter",
label = "",
icon = icon("sync-alt"),
color ="success",
style ="gradient",
size = "sm"
)
),
column(width = 4,
#reset genotype
shinyWidgets::actionBttn(
inputId = "reset_genotype_filter",
label = "",
icon = icon("sync-alt"),
color = "success",
style ="gradient",
size = "sm"
)
)
),
hr(),
## select all rows
shinyWidgets::checkboxGroupButtons(
inputId = "sra_sample_info_select_all_rows",
label = "",
choices = c("Select all rows" = TRUE),
status = "success",selected = FALSE,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
br(), br(),
## SRA info table
div(DT::dataTableOutput(outputId = "pre_loaded_data_sra_sample_info" , width = "auto") %>%
shinycssloaders::withSpinner(color = "#18BC9C") , style = "font-size:80%"),
br(), br(),
## Display number of rows selected
fluidRow(
column(width = 12,offset =5,
tags$h3(tags$b(textOutput(outputId = "sra_info_number_of_rows_selected")))
)
),
br(), br(),
fluidRow(
## clear all
column(width = 4,offset = 3,
shinyWidgets::actionBttn(inputId = "deselect_all_rows",
label = "Clear all" ,
size = "md" ,
style = "gradient",
icon = icon("times-circle"),
color = "success")
),
## submit
column(width = 4,
shinyWidgets::actionBttn(inputId = "submit_user_sra_samples",
label = "Submit" ,
size = "md",
style = "gradient" ,
icon = icon("thumbs-up"),
color = "success")
)
)
),
## upload data action button
conditionalPanel(
condition = "input.data_selection =='upload_user_data'",
shinyWidgets::actionBttn(
inputId = "upload_sample_trigger",
label = "Upload", color = "success",
style = "gradient", size = "md",
icon = icon("upload"), block = T
)
),
## upload data trigger
shinyBS::bsModal(size = "large",
id = "trigger_upload_user_data", title = "Upload Data",
trigger = "upload_sample_trigger",
## upload sample data checkbox
shinyWidgets::materialSwitch(
inputId = "upload_sample_data",
label = tags$b("Upload example data"),
value = FALSE,
status = "info"
),
shinyWidgets::progressBar(id = "upload_sample_data_pb", value = 0, status = "success", striped = TRUE),
hr(),
##upload data, either from file or from clipboard
tags$div(id = "user_data_upload_section",
tags$h2(tags$b("Step 1: Upload data")),
wellPanel(
fluidRow(
column(width = 12,
radioButtons(inputId = "upload_data_source" , label = "",
choices = c("From file" = "upload_from_file", "From clipboard" = "upload_from_clipboard"),
width = "100%",inline = T,
)
)
),
fluidRow(
conditionalPanel(condition = "input.upload_data_source == 'upload_from_file'",
column(width = 12,
fileInput(
inputId = "file1",
label = "",
#label = tags$h3(tags$b("Read from file")), #"Choose .txt file",
multiple = F,width = "100%",placeholder = "Upload .txt file",
accept = c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv"
)
)
)
),
conditionalPanel(condition = "input.upload_data_source == 'upload_from_clipboard'",
column(width = 12,
textAreaInput(placeholder = "Paste data here",
inputId = "user_pasted_data",
label = "",cols = 10, rows = 10
#label = tags$h3(tags$b("Read from file")), #"Choose .txt file",
#multiple = F,width = "100%",placeholder = "Upload .txt file",
)
)
)
),
tags$div(id = "file_instruct", tags$h4(tags$b("Data uploading instructions")), "While uploding data from file, file must be of .txt format. Columns are variables (e.g. sample names) and rows are observations (e.g. genes). Each column and row must have unique identity given as first row and first column respectively. Same rules also appy while pasting data from clipboard.")
),
## choice of column seperator
tags$h2(tags$b("Step 2: Select column separator")),
wellPanel(
radioButtons(
inputId = "sep",
label = "",
width = "100%",
choices = c(
Comma = ",",
Semicolon = ";",
Tab = "\t"
),
selected = "\t",
inline = T
)
),
## select species
tags$h2(tags$b("Step 3: Select species (optional)")),
tags$h5(tags$i(
"Corrrect species selection is required for gene annotations and GO analysis."
)),
br(),
wellPanel(
shinyWidgets::pickerInput(
inputId = "user_selected_species",
label = "",
choices = rlang::set_names(species_table$genome , species_table$species),
selected = "FungiDB-66_AnidulansFGSCA4",
choicesOpt = list(
style = "btn-primary",
subtext = species_table$genome),
options = list(`showSubtext` = TRUE)
),
## show random gene id for selected species
tags$div( tags$h4(tags$b("Values in the first column of file being uploaded must have below id type :")) ,
textOutput(outputId = "sample_selected_species_gene_id") %>%
shinycssloaders::withSpinner(color = "#18BC9C"))
),
## log transformation
tags$h2(tags$b("Step 4: Log transformation (optional)")),
wellPanel(
radioButtons(inputId = "log_transform_user_upload_data" ,
label = "",
choices = c("None" = "none" ,
"Log2(value + 1)" = "log2" ,
"Log10(value + 1)" = "log10"),
selected = "none",inline = T
)
),
# decide whether user data to join with existing data
tags$h2(tags$b("Step 5: Join data (optional)")),
wellPanel(
shinyWidgets::materialSwitch(
inputId = "join_user_data",
label = ,
value = FALSE,
status = "success"
),
## join data
tags$div(id = "join_data_instruction",
tags$b("Join data"),
"feature allows users to merge user uploaded data with pre existing data if selected any. Uploaded dataset will be merge by gene names given in the first column."),
br()
),
## submit
fluidRow(
column(width = 4 , offset = 5,
shinyWidgets::actionBttn(inputId = "submit_user_uploaded_data" ,
label = "Submit" ,
icon = icon("thumbs-up") ,
style = "gradient",
color = "success" ,
size = "md" ,
block = F)
)
)
)
)
)
),
hr(),
## Assign groups
shinyBS::bsCollapse(id = "assing_gene_groups_and_sample_groups",
open = "Assign groups",
shinyBS::bsCollapsePanel(title = "Assign groups", style = "primary",
add_sample_group_ui(id = "sample_group"),
br(),
add_gene_groups_ui(id = "gene_groups")
)
),
hr(),
## Display active group info in the side panel
conditionalPanel(condition = "true" ,
shinyBS::bsCollapse(id = "display_active_group_collapse_panel",
open = "View active groups",
shinyBS::bsCollapsePanel(title = "View active groups",
style = "primary" ,
display_active_groups_ui(id = "display_active_groups")
)
)
),
## Display user selected sra id sample info
conditionalPanel(condition = "output.display_sra_sample_info_in_side_panel==true" ,
shinyBS::bsCollapse(id = "display_sra_sample_info_collapse_panel",
open = "View SRA sample info",
shinyBS::bsCollapsePanel(title = "View SRA sample info",
style = "primary",
display_sra_sample_info_ui(id = "user_selected_sra_id_sample_info")
)
)
),
br(),
## display website statistics in side panel
shinyBS::bsCollapse(id = "display_live_statistics",
open = "Usage",
shinyBS::bsCollapsePanel(title = "Usage",
style = "primary",
tags$div(
HTML("<script type=\"text/javascript\" src=\"//rf.revolvermaps.com/0/0/7.js?i=5cen61amuqv&m=0&c=ff0000&cr1=ffffff&sx=0\" async=\"async\"></script>")
)
)
)
## upload data ends
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## UI main panel
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
mainPanel(
width = 9,
tabsetPanel(
type = "tabs",
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## scatter plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Scatter plot", value = "scatter_plot_panel", id = "scatter_plot_panel",
## select plot varibale
h3(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
multiple = T, open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select plot variable
fluidRow(
column(width = 6,
## select x variable
shinyWidgets::pickerInput(
inputId = "scatter_x",
label = "Select sample (X-axis)",
choices = NULL,
choicesOpt = F,
selected = "",
multiple = F, width = "100%",
options = list(
`actions-box` = TRUE,
style = "btn-success", `live-search` = TRUE
)
)
),
column(width = 6,
## select y variable
shinyWidgets::pickerInput(
inputId = "scatter_y",
label = "Select sample (Y-axis)",
choices = NULL, choicesOpt = F,
selected = "", multiple = F, width = "100%",
options = list(
`actions-box` = TRUE,
style = "btn-success", `live-search` = TRUE
)
)
)
),
## select gene groups
gene_group_selection_ui(id = "scatter_plot_select_gene_groups"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_scatter" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
# plot output
conditionalPanel(
condition = "input.generate_scatter && output.scatter_plot_status==true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty column
column(
width = 8,
plotOutput(outputId = "scatter_plot",
brush = "plot_brush", height = "auto", width = "auto")
),
column(width = 2) ## empty column
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## scatter plot advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
hr(),
# column(width = 1), ## empty column
column(
#offset = 1,
width = 12,
## scatter plot Labels & Title button
column(
width = 6,
plot_title_and_axis_label_ui(id = "scatter_plot_title_and_labels")
),
## scatter plot Advance options
column(
width = 3,
shinyWidgets::dropdownButton(
inputId = "scatter_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
h4(tags$b("Axis limits")),
actionLink(
inputId = "trigger_scatter_xy_limits", label = "Set",
icon = icon(name = "edit", lib = "font-awesome")
),
hr(),
## scatter plot trend line
shinyWidgets::radioGroupButtons(
inputId = "scatter_diagonal_line",
label = h4(tags$b("Trend line")),
choices = c(
"Off" = "off",
"From data" = "from_data",
"Manual" = "manual"
),
individual = TRUE ,
justified = T, width = "400px",
status = "success" ,
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## manual slope
conditionalPanel(
condition = "input.scatter_diagonal_line == 'manual'",
fluidRow(
column(
width = 6,
numericInput(inputId = "manual_slope", label = h4(tags$b("Slope")), value = 1)
),
column(
width = 6,
numericInput(inputId = "manual_intercept", label = h4(tags$b("Intercept")), value = 0)
)
)
),
hr(),
# color selection
shinyWidgets::radioGroupButtons(
inputId = "scatter_color_chooser",
label = h4(tags$b("Color by")), choices = c("Density" = "default",
"Manual" = "manual" ,
"Gene group"="by_gene_groups"),
individual = TRUE ,
justified = T , width = "400px",
status = "success" ,size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## color : low
conditionalPanel(
condition = "input.scatter_color_chooser == 'manual'",
fluidRow(
column(
width = 4,
colourpicker::colourInput(
inputId = "scatter_col_low",
label = "low",
value = "blue",
returnName = TRUE
)
),
## color : med
column(
width = 4,
colourpicker::colourInput(
inputId = "scatter_col_medium",
label = "med",
value = "yellow",
returnName = TRUE
)
),
## color : high
column(
width = 4,
colourpicker::colourInput(
inputId = "scatter_col_high",
label = "high",
value = "red",
returnName = TRUE
)
)
)
),
hr(),
## transparancy
sliderInput(
inputId = "scatter_alpha",
label = h4(tags$b("Transparency")), min = 0, max = 1, value = 0.5, step = 0.01, width = "99%"
),
hr(),
## adjust dot size
sliderInput(
inputId = "scatter_point_size",
label = h4(tags$b("Point size")), min = 1, max = 10, value = 2, step = 0.1,width = "99%"
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_scatter")
)
)
)
)
),
### Triggered actions
## set X-Y limits
shinyBS::bsModal(
id = "scatter_xy_limits", title = "Set axis limits", trigger = "trigger_scatter_xy_limits",
column(
width = 6,
## X-lim
numericInput(inputId = "plot_xmin", label = "X-Min:", value = ""),
numericInput(inputId = "plot_xmax", label = "X-Max:", value = "")
),
column(
width = 6,
## Y-lim
numericInput(inputId = "plot_ymin", label = "Y-Min:", value = ""),
numericInput(inputId = "plot_ymax", label = "Y-Max:", value = "")
)
)
### set X-Y limits ends
),
## scatter plot table output
conditionalPanel(
condition = "output.scatter_plot && input.plot_brush",
#downloadButton(outputId = "download_scatter_data", label = "", icon = icon("download")),
## scatter plot data or functional analysis
radioGroupButtons(
inputId = "scatterplot_data_or_functional_analysis",
choices = c("Show Data" = "show_scatterplot_data",
"Functional Analysis" = "scatterplot_functional_analysis"),
status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon")) ,
size = "normal" ,
direction = "horizontal" ,
justified = TRUE ,
individual = TRUE ,selected = "",
width = "100%"
),
br(),
## show scatter plot brushed data
conditionalPanel(
condition = "input.scatterplot_data_or_functional_analysis == 'show_scatterplot_data'",
shinyBS::bsCollapse(
open = "Selected points",
shinyBS::bsCollapsePanel(
title = "Selected points", style = "primary",
DT::dataTableOutput(outputId = "brush_table", width = "auto") %>%
shinycssloaders::withSpinner( color = "#18BC9C")
)
)
),
## show scatter plot functional analysis
conditionalPanel(
condition = "input.scatterplot_data_or_functional_analysis == 'scatterplot_functional_analysis'",
shinyBS::bsCollapse(
open = "Functional analysis",
shinyBS::bsCollapsePanel(
title = "Functional analysis", style = "primary",
functional_analysis_ui(id = "scatterplot_functional_analysis_ui")
)
)
)
)
),
## scatter plot tab panel ends
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## multi scatter plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Multi-scatter plot", value = "multi_scatter_plot_panel", id = "multi_scatter_plot_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
# select plot variables
shinyWidgets::pickerInput(
inputId = "multi_scatter_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
# select gene groups
gene_group_selection_ui("multi_scatter_plot_gene_group_selection"),
## plot action
# actionButton(
# inputId = "generate_multi_scatter",
# label = "Plot"
# )
hr(),
## plot action
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_multi_scatter" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
conditionalPanel(
condition = "input.generate_multi_scatter && output.multi_scatter_plot_status==true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty column
column(
width = 8,
plotOutput(outputId = "multi_scatter_plot", height = "auto", width = "auto")
),
column(width = 2) ## empty column
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## multi scatter plot advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
hr(),
# column(width = 1), ## empty column
column(
width = 12,
## multi scatter labels and Titles
column(
width = 6,
plot_title_and_axis_label_ui(id = "multi_scatter_plot_title_and_labels")
),
## multi scatter Advance options
column(
width = 3,
dropdownButton(
inputId = "multi_scatter_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
## corr text color
colourpicker::colourInput(
inputId = "multi_scatter_corr_text_col",
label = tags$h4(tags$b("Corr text color")),
value = "red",
returnName = TRUE,
palette = "limited"
),
## corr text font size
sliderInput(
inputId = "multi_scatter_corr_text_text_size", label = tags$h4(tags$b("Font size: Corr text")),
min = 1, max = 30, value = 5, step = 1
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_multi_scatter")
)
)
# column(width = 1) ## empty column
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Corr heatbox panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "CorrHeatBox", value = "corr_heatbox_panel", id = "corr_heatbox_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## corr heat box : select plot variables
shinyWidgets::pickerInput(
inputId = "corr_heatbox_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## corr heat box : select gene groups
gene_group_selection_ui("corr_heat_box_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_corr_heatbox" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
conditionalPanel(
condition = "input.generate_corr_heatbox && output.corr_heatbox_status == true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty column
column(
width = 8,
plotOutput(outputId = "corr_heatbox", height = "auto", width = "auto")
),
column(width = 2) ## empty column
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## corr_heatbox advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
column(
width = 12,
## corr_heatbox labels and Titles
column(
width = 6,
plot_title_and_axis_label_ui(id = "corr_heatbox_title_and_labels")
),
## corr_heatbox Advance options
column(
width = 3,
dropdownButton(
inputId = "corr_heatbox_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = F,
sliderInput(inputId = "corr_heatbox_colors" ,
label = "Number of colors" ,
value = 5,min = 1,
max = 5,
step = 1,
width = "100%"),
hr(),
## Cluster by correlation
shinyWidgets::radioGroupButtons(inputId = "cluster_heatbox" ,
label = tags$h4(tags$b("Cluster variables")),
choices = c("TRUE" = TRUE , "FALSE" = FALSE),
selected = TRUE,
width = "100%",
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success" ,
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## heatbox method
shinyWidgets::radioGroupButtons(inputId = "heatbox_method" ,
label = tags$h4(tags$b("Method")),
choices = c("Circle" ="circle" ,
"Square" = "square") ,
selected = "square",
width = "100%",
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success",
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## heatbox type
shinyWidgets::radioGroupButtons(inputId = "heatbox_type" ,
label = tags$h4(tags$b("Type")),
choices = c("Full" ="full" , "Upper" = "upper" , "Lower" = "lower"),
width = "100%",
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success",
size = "sm" ,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
conditionalPanel(
condition = "input.heatbox_type != 'full'",
## show diagonal
shinyWidgets::radioGroupButtons(inputId = "heatbox_show_diag" ,
label = tags$h4(tags$b("Show diagonal")),
choices = c("TRUE" = TRUE , "FALSE" = FALSE),
selected = "TRUE",
width = "100%" ,
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success" ,
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
hr(),
## corr heatbox scale choice
shinyWidgets::radioGroupButtons(inputId = "corr_heatbox_scale_manual" ,
label = tags$h4(tags$b("Scale")) ,
choices = c("Auto" = "auto" , "Manual" = "manual") ,
selected = "auto" ,
width = "100%" ,
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success",
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## corr heat box manual color scale
conditionalPanel(condition = "input.corr_heatbox_scale_manual == 'manual'" ,
fluidRow(
column(
width = 6,
numericInput(inputId = "corr_heatbox_scale_manual_min" ,
label = "Scale low",
value = -1, min = -1, max = 1,step = 0.1,width = "100%")
),
column(width = 6,
numericInput(inputId = "corr_heatbox_scale_manual_max" ,
label = "Scale high",
value = 1,
min = -1,
max = 1,
step = 0.1,width = "100%")
)
)
),
hr(),
## show / hide corr value
shinyWidgets::radioGroupButtons(
inputId = "heatbox_show_corr_value" ,
label = tags$h4(tags$b("Show corr value")),
choices = c("TRUE"= TRUE, "FALSE" = FALSE),
selected = FALSE ,
width = "100%",
direction = "horizontal",
individual = TRUE ,
justified = T,
status = "success",
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
# checkboxInput(inputId = "heatbox_show_corr_value" ,
# label = "Show corr value",value = FALSE , width = "100%"),
hr(),
## corr text font size
sliderInput(
inputId = "heatbox_corr_text_text_size",
label = "Font size: Corr text",width = "100%",
min = 1, max = 30, value = 5, step = 0.1
),
hr(),
## corr text color
colourpicker::colourInput(
inputId = "heatbox_corr_text_col",
label = "Corr text color",
value = "yellow",
returnName = TRUE
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_corr_heatbox")
)
)
# column(width = 1) ## empty column
)
)
)
),
## show corr heatbox data
conditionalPanel(condition = "input.generate_corr_heatbox && output.corr_heatbox_status == true",
shinyBS::bsCollapse(
open = "CorrHeatboxData",
shinyBS::bsCollapsePanel(
title = "CorrHeatboxData",
style = "primary",
DT::dataTableOutput(outputId = "corr_heatbox_data", width = "auto") %>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## density plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Density plot", value = "density_plot_panel", id = "density_plot_panel",
br(),
## select x variables
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select density plot variables
shinyWidgets::pickerInput(
inputId = "density_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## density gene group selection
gene_group_selection_ui("density_plot_gene_group_selection"),
## plot action
hr(),
column(width =6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_density" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display density plot
conditionalPanel(
condition = "input.generate_density && output.density_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty col
## plot output column
column(
width = 8,
plotOutput(outputId = "density_plot", height = "auto")
),
column(width = 2) ## empty col
),
## density plot advanced setting buttons
fluidRow(
hr(),
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "decorate_density_plot")
),
column(
width = 3,
dropdownButton(
inputId = "density_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
## fill and facet density plot
ggplot_fill_and_facet_ui(id = "density_plot_fill_and_facet"),
## density transparency
sliderInput(
inputId = "density_plot_alpha",
label = tags$h4(tags$b("Transparency")), min = 0, max = 1, value = 0.5, step = 0.01, width = "99%"
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_density")
)
)
)
)
)
)
),
## density plot tab panel ends
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## histogram ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Histogram", value = "histogram_panel", id = "histogram_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select histogram variables
shinyWidgets::pickerInput(
inputId = "histogram_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
`live-search` = TRUE,
style = "btn-success"
)
),
gene_group_selection_ui("histogram_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_histogram" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display histogram
conditionalPanel(
condition = "input.generate_histogram && output.histogram_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty col
## plot output column
column(
width = 8,
plotOutput(outputId = "histogram", height = "auto")
),
column(width = 2) ## empty col
),
## histogram advanced options
fluidRow(
hr(),
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "decorate_histogram")
),
column(
width = 3,
dropdownButton(
inputId = "histogram_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
ggplot_fill_and_facet_ui(id = "histogram_fill_and_facet"),
## hitogram position choices.
selectInput(
inputId = "histogram_positions",choices = c("Dodge" = "dodge" , "Stack" = "stack" , "Identity" = "identity"),
label = tags$h4(tags$b("Bar positions")) ,
selected = "dodge",multiple = FALSE, width = "100%"
),
hr(),
## histogram number of bins
numericInput(
inputId = "histogram_number_of_bins",
label = tags$h4(tags$b("Number of bins")), value = 30 , min = 1, max = 1000 , step = 1,
width = "100%"
),
hr(),
## histogram Transparency
sliderInput(
inputId = "histogram_alpha",
label = tags$h4(tags$b("Transparency")), min = 0, max = 1, value = 0.5, step = 0.01 , width = "99%"
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_histogram")
)
)
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Joy plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Joy plot", value = "joy_plot_panel", id = "joy_plot_panel",
br(),
## select x variables
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select joy plot variables
shinyWidgets::pickerInput(
inputId = "joy_plot_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## joy plot gene groups
gene_group_selection_ui("joy_plot_gene_group_selection"),
## plot action
hr(),
column(width =6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_joy_plot" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display Joy plot
conditionalPanel(
condition = "input.generate_joy_plot && output.joy_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty col
## plot output column
column(
width = 8,
plotOutput(outputId = "joy_plot", height = "auto")
),
column(width = 2) ## empty col
),
## joy plot settings
fluidRow(
hr(),
## joy plot labels and title
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui("decorate_joy_plot")
),
## joy plot advance settings
column(
width = 3,
dropdownButton(
inputId = "joy_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,width = "450px",
br(),
## joyplot fill and facet UI
joy_plot_fill_and_facet_ui("joy_plot_fill_and_facet")
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_joy_plot")
)
)
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## box plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Box plot", value = "box_plot_panel", id = "box_plot_panel",
br(),
## select plot varibale
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select x variable
shinyWidgets::pickerInput(
inputId = "box_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success" , `live-search` = TRUE
)
),
gene_group_selection_ui("box_plot_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_box" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display box plot
conditionalPanel(
condition = "input.generate_box && output.box_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty cols
## display box plot
column(
width = 8,
plotOutput(outputId = "box_plot", height = "auto", width = "auto")
),
column(width = 2) ## empty cols
),
## box plot setting options.
fluidRow(
hr(),
column(width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "box_plot_label_and_title")
),
## box plot advance options.
column(
width = 3,
dropdownButton(
inputId = "box_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
## fill and facet ui
ggplot_fill_and_facet_ui(id = "box_plot_fill_and_facet"),
## pvalue
radioGroupButtons(
inputId = "box_plot_pvalue",
label = tags$h4(tags$b("P-value")) ,
size = "sm" , individual = T,
justified = T,
status = "success",
choices = c("Hide" = "FALSE", "Show" = "TRUE"),
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## pvalue method
conditionalPanel(
condition = "input.box_plot_pvalue == 'TRUE'",
selectInput(
inputId = "box_plot_pval_method",
label = tags$h4(tags$b("Method")),
choices = c("t.test" = "t.test", "wilcox.test" = "wilcox.test")
)
),
hr(),
## box plot dots
radioGroupButtons(
inputId = "box_plot_show_dots",
label = tags$h4(tags$b("Dots")) ,
size = "sm" , individual = T,
justified = T,
status = "success",
choices = c("Hide" = "FALSE", "Show" = "TRUE"),
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## box plot dots related UI
conditionalPanel("input.box_plot_show_dots =='TRUE'",
##box plot dots width
sliderInput(inputId = "boxplot_dots_width" ,
label = tags$h4(tags$b("Dots width")),
min = 0.1,
max = 1,
value = 0.1,
step = 0.01,width = "99%"
),
## box plot dots color
colourpicker::colourInput(
inputId = "boxplot_dots_color",
label = tags$h4(tags$b("Dots color")),
value = "black",
returnName = TRUE
),
## box plot dots transparency
sliderInput(inputId = "boxplot_dots_transprancy" ,
label = tags$h4(tags$b("Dots transparency")),
min = 0.1,
max = 1,
value = 0.5,
step = 0.01,
width = "99%"
)
),
## Box transparacny
sliderInput(
inputId = "box_plot_alpha",
label = tags$h4(tags$b("Box transparency")) ,
min = 0,
max = 1,
value = 0.5,
step = 0.01,
width = "99%"
),
hr()
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_box_plot")
)
))
)
)
)
),
## box plot tab panel ends
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## violin plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Violin plot", value = "violin_plot_panel", id = "violin_plot_panel",
br(),
## select plot varibale
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select x variable
shinyWidgets::pickerInput(
inputId = "violin_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## violin plot gene group selection
gene_group_selection_ui("violin_plot_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_violin" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## display violin plot
conditionalPanel(
condition = "input.generate_violin && output.violin_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty cols
## display violin plot
column(
width = 8,
plotOutput(outputId = "violin_plot", height = "auto", width = "auto")
),
column(width = 2) ## empty cols
),
## violin plot setting options.
fluidRow(
hr(),
column(width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "violin_plot_label_and_title")
),
## violin plot advance options.
column(
width = 3,
dropdownButton(
inputId = "violin_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
# # fill violin
# shinyWidgets::radioGroupButtons(
# inputId = "fill_violin_plot",
# label = tags$h4(tags$b("Fill by")),
# choices = c("Samples" = "samples", "Sample groups" = "groups" ,
# "Identical" = "identical") ,
# selected = "samples" ,status = "success" ,size = "sm",
# direction = "horizontal",
# individual = TRUE ,
# justified = T,
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
#
# ## fill violin manually
# conditionalPanel(
# condition = "input.fill_violin_plot == 'identical'",
# fluidRow(
# column(
# width = 4,
# colourpicker::colourInput(
# inputId = "violin_plot_color_chooser",
# label = tags$h4(tags$b("Select")) ,
# value = "black",
# returnName = TRUE,
# palette = "limited"
# )
# )
# )
# ),
#
# hr(),
ggplot_fill_and_facet_ui(id = "violin_plot_fill_and_facet"),
# ## pvalue
radioGroupButtons(
inputId = "violin_plot_pvalue",
label = "P-value",
size = "sm" ,
individual = T, justified = T,
status = "success",
choices = c("Hide" = "FALSE", "Show" = "TRUE"),
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## pvalue method
conditionalPanel(
condition = "input.violin_plot_pvalue == 'TRUE'",
selectInput(
inputId = "violin_plot_pval_method",
label = "Method",
choices = c("t.test" = "t.test", "wilcox.test" = "wilcox.test")
)
),
hr(),
## show quantiles lines
shinyWidgets::checkboxGroupButtons(inputId = "violin_show_quantile" ,
label = tags$h4(tags$b("Show quantile")) ,
choices = c("0.1"=0.1, "0.25"=0.35, "0.5"=0.5 , "0.75"=0.75 , "0.9"=0.9) ,
width = "100%",
selected = 0.5 ,
status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T
),
hr(),
# ## flip violin
# shinyWidgets::radioGroupButtons(
# inputId = "violin_flip_xy",
# label = h4(tags$b("Flip axis")),
# choices = c("TRUE" = TRUE, "FALSE" = FALSE),
# selected = "FALSE" , status = "success" ,size = "sm",
# direction = "horizontal",
# individual = TRUE ,
# justified = T,
# width = "300px",
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
# hr(),
# ## facetting
# shinyWidgets::radioGroupButtons(
# inputId = "violin_facet_groups",
# label = h4(tags$b("Separate groups")),
# choices = c("TRUE" = TRUE, "FALSE" = FALSE),
# selected = "FALSE" , status = "success" ,size = "sm",
# direction = "horizontal",
# individual = TRUE ,
# justified = T,
# width = "300px",
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
# hr(),
#
## alpha
sliderInput(
inputId = "violin_plot_alpha",
label = tags$h4(tags$b("Transparency")),
min = 0,
max = 1, value = 0.5, step = 0.01, width = "99%"
),
hr()
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_violin_plot")
)
))
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## bar plot panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Bar plot", value = "barplot_panel", id = "barplot_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
shinyWidgets::pickerInput(
inputId = "barplot_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## select genes to include in the bar plot.
shinyWidgets::pickerInput(
inputId = "barplot_select_genes",
label = "Select genes(s)",
choices = NULL,
choicesOpt = F,
selected = "",
multiple = T,
width = "100%",
options = list(
size = 10,
`selected-text-format` = "count > 10",
`live-search` = TRUE,
style = "btn-success"
)
),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_barplot" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
conditionalPanel(
condition = "input.generate_barplot && output.barplot_status == true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 2), ## empty column
column(
width = 8,
plotOutput(outputId = "barplot", height = "auto", width = "auto")
),
column(width = 2) ## empty column
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## bar plot advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
hr(),
column(width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "barplot_label_and_title")
),
##
column(
width = 3,
dropdownButton(
inputId = "barplot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
br(),
## xaxis : genes, or sample
shinyWidgets::radioGroupButtons(
inputId = "barplot_xaxis_choices",
label = h4(tags$b("X-axis")),
choices = c("Genes" = "GeneNames" ,"Samples" = "samples") ,
selected = "GeneNames" ,status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,
width = "400px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon")),
),
hr(),
# bar plot fill bars
shinyWidgets::radioGroupButtons(
inputId = "fill_barplot",
label = h4(tags$b("Fill by")),
choices = c("Manual" = "identical",
"Genes" = "GeneNames" ,"Samples" = "samples",
"Sample groups" = "groups") ,
selected = "samples" ,status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,
width = "400px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## fill bars manually
conditionalPanel(
condition = "input.fill_barplot == 'identical'",
fluidRow(
column(
width = 4,
colourpicker::colourInput(
inputId = "barplot_color_chooser",
label = h4(tags$b("Select")),
value = "black",
returnName = TRUE
)
)
)
),
hr(),
## facetting
shinyWidgets::radioGroupButtons(
inputId = "barplot_facet_value",
label = h4(tags$b("Separate by")),
choices = c("None" = "none" ,
"Genes" = "GeneNames" ,
"Samples" = "samples",
"Sample groups" = "groups"),
selected = "none",status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,
width = "400px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## Y scale during facetting
shinyWidgets::radioGroupButtons(
inputId = "barplot_yscale",
label = h4(tags$b("Scale")),
choices = c("Fix" = "fixed" , "Free" = "free",
"Free X" = "free_x" , "Free Y" = "free_y"),
selected = "fixed",status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,width = "400px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## alpha
sliderInput(
inputId = "barplot_alpha",
label = h4(tags$b("Transparency")),
min = 0,
max = 1,
value = 0.5, step = 0.01, width = "99%"
)
)
),
## export plot as image
column(
width = 3,
export_plot_ui(id = "export_barplot")
)
)
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## PCA plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "PCA plot", value = "pca_plot_panel", id = "pca_plot_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
# PCA plot select variables
shinyWidgets::pickerInput(
inputId = "pca_plot_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE ,
selectOnTab = TRUE
)
),
gene_group_selection_ui("pca_plot_gene_group_selection"),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_pca_plot" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
conditionalPanel(
condition = "input.generate_pca_plot && output.pca_plot_status == true",
shinyBS::bsCollapse(
multiple = T, open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
#column(width = 2), ## empty column
column(
width = 9,
plotOutput(outputId = "pca_plot",
brush = "pca_plot_brush",
height = "auto",
width = "auto") #%>% shinycssloaders::withSpinner(color = "#18BC9C")
),
### show / hide sample groups
column(width = 3 ,
shinyWidgets::multiInput(width = "100%",
inputId = "pca_plot_hide_sample_groups",
label = "Show / Hide sample groups",
choices = "") %>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## PCA plot advanced options
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
fluidRow(
hr(),
# column(width = 1), ## empty column
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "decorate_pca_plot")
),
column(
width = 3,
## PCA Advance options drop down menu.
dropdownButton(
inputId = "pca_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
## select PCs
shiny::selectizeInput("select_pcs_to_plot", label="Select PCs",
choices=NULL,
multiple=TRUE ,
options = list(maxItems = 2)),
## display / hide sample names
shinyWidgets::radioGroupButtons(inputId = "pca_display_sample_names",
label = tags$h4(tags$b("Disply sample names")) ,
choices = c("TRUE" = TRUE, "FALSE" = FALSE),
selected = "FALSE",status = "success" ,
size = "sm",
direction = "horizontal", individual = TRUE ,
justified = T,
width = "300px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## PCA sample names size .
conditionalPanel(condition = "input.pca_display_sample_names == 'TRUE'" ,
sliderInput(
inputId = "pca_plot_sample_names_size",
label = tags$h4(tags$b("Font size: Sample names")),
min = 1,
max = 10,
value = 5,
step = 0.05
),
hr()
),
## PCA dot size.
sliderInput(inputId = "pca_sample_dot_size" ,
label = tags$h4(tags$b("Dot size")),
min = 1,
max = 10,
value = 5,
step = 0.05),
hr(),
## pca colors
shinyWidgets::radioGroupButtons(inputId = "pca_plot_colour" ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
label = tags$h4(tags$b("Color by")) ,
choices = c("Identical"="identical",
"Sample groups" = "groups" ,
"K-means" = "kmeans") ,
selected = "identical" ,
width = "300px",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr(),
## color choices color identical
conditionalPanel(condition = "input.pca_plot_colour == 'identical' " ,
colourpicker::colourInput(
inputId = "pca_sample_name_color",
label = tags$h4(tags$b("Select color")),
value = "black",
returnName = TRUE
)
),
## color choices color identical
conditionalPanel(condition = "input.pca_plot_colour == 'kmeans' " ,
shiny::numericInput(inputId = "pca_sample_sample_kmeans_n" ,
label = "Number of cluster" ,
value = 1 , step = 1, min = 1, max = 100)
)
)
),
## export plot as imagess
column(
width = 3,
export_plot_ui(id = "export_pca_plot")
)
)
)
)
),
### Triggered actions
## set axis and plot titles
shinyBS::bsModal(
id = "pca_plot_edit_titles", title = "Title and labels", trigger = "trigger_pca_plot_edit_titles",
## plot titles
h4(tags$b("Title")),
textInputIcon(inputId = "pca_plot_title",
label = "",
value = "",
placeholder = "Main :"),
hr()
)
),
### pca plot brushed points datatable
fluidRow(
column(width = 12,
conditionalPanel(
condition = "output.pac_plot_brushed_data_table_status==true",
shinyBS::bsCollapse(
open = "Selected SRA points sample information (Does not apply to user uploaded data)",
shinyBS::bsCollapsePanel(
title = "Selected SRA points sample information (Does not apply to user uploaded data)", style = "primary",
DT::dataTableOutput(outputId = "pca_brushed_datatable", width = "auto") %>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
)
)
)
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## line plot tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Line plot", value = "line_plot_panel", id = "line_plot_panel",
br(),
## select plot varibale
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
## select x variable
shinyWidgets::pickerInput(
inputId = "lineplot_x",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## select line plot gene groups
gene_group_selection_ui(id = "line_plot_gene_group_selection"),
hr(),
fluidRow(
column(width = 12,
## line plot gene selection
shinyWidgets::radioGroupButtons(
inputId = "lineplot_genes_selection",
label = tags$h4(tags$b("Genes to plot")),
choices = c("# top variable genes (By standard deviation)" = "top_variable_genes", "All genes" = "all"),
individual = T,
justified = T,
status = "success" ,
size = "sm" ,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## number of top variable genes for lineplot
conditionalPanel(
condition = "input.lineplot_genes_selection == 'top_variable_genes'",
numericInput(
inputId = "lineplot_top_n_genes",
label = tags$h4(tags$b("# top variable genes to show")),
value = 500, min = 50, max = 2000, step = 50 #width = "100%"
)
),
hr(),
## line plot clustering
shinyWidgets::radioGroupButtons(
inputId = "line_plot_cluster_genes_by",
label = tags$h4(tags$b("Gene cluster")),
choices = c("K-means" = "kmeans",
"Gene groups" = "gene_groups"),
individual = T,
justified = T,
status = "success" ,
size = "sm" ,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## line plot number of k-means cluster
conditionalPanel(
condition = "input.line_plot_cluster_genes_by == 'kmeans'",
numericInput(
inputId = "line_plot_nclust",
label = tags$h4(tags$b("# of clusters (k-means)")),
value = 5, min = 1, max = 10, step = 1
)
),
hr(),
## line plot choice for value to use in cluster
fluidRow(
column(
width = 6,
shinyWidgets::radioGroupButtons(
inputId = "lineplot_cluster_value_type",
label = tags$h4(tags$b("Cluster by")),
choices = c("Raw value" = "raw_val" ,
"Z-Score" = "zscore"),
selected = "zscore", justified = T,
size = "sm" ,
status = "success",
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
## line plot choice of value to display
column(
width = 6,
shinyWidgets::radioGroupButtons(
inputId = "lineplot_display_value_type",
label = tags$h4(tags$b("Display value")),
choices = c("Raw value" = "raw" , "Z-Score" = "zscore"),
selected = "zscore",
size = "sm" ,
justified = T,
status = "success",
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
)
),
hr(),
## all lines or average line
shinyWidgets::radioGroupButtons(inputId = "activate_avg_line_plot" ,
label = tags$h4(tags$b("Display lines for")) ,
choices = c("Individual gene" = "individual" , "Average of all"= "average" ) ,
selected = "individual",
size = "sm" ,
width = "100%" ,
justified = T,
individual = T,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon")),
status = "success"),
## average line type : mean or median
conditionalPanel(
"input.activate_avg_line_plot == 'average'",
shinyWidgets::radioGroupButtons(inputId = "avg_line_type" ,
label = "Average type" ,
choices = c("Mean" = "mean",
"Median" = "median") ,
selected = "median",
size = "sm" ,
width = "100%" ,
justified = T,
individual = T,
status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
)
)
),
## plot action
hr(),
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_lineplot" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
),
## line plot plot panel
conditionalPanel(
condition = "input.generate_lineplot && output.line_plot_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(
column(width = 1), ## empty column
## display line plot
column(
width = 10, #style = "overflow-y:auto;",
plotOutput(outputId = "line_plot",
height = "auto",
width = "auto")),
column(width = 1) ## empty column
),
## line plot advance options
fluidRow(
hr(),
## line plot title and labels
column(
width = 12,
column(
width = 6,
plot_title_and_axis_label_ui(id = "decorate_line_plot")
),
## line plot Advance options
column(
width = 3,
dropdownButton(
inputId = "line_plot_options",
icon = icon("cogs"),
label = "Advance options",
size = "sm",
circle = F,
status = "success",
up = T,
right = T,
## line plot color choices
shinyWidgets::radioGroupButtons(
inputId = "line_plot_color_by",
label = tags$h4(tags$b("Color")),
choices = rlang::set_names(c("gene_groups","identical") ,
c("Gene groups", "Identical")),
individual = T,
justified = T,
status = "success" ,
size = "sm" ,
width = "300px"
),
## line plot color indentical
conditionalPanel(
condition = paste0("input.line_plot_color_by == 'identical'"),
fluidRow(
column(
width = 4,
colourpicker::colourInput(
inputId = "line_plot_color_chooser",
label = tags$h4(tags$b("Select")),
value = "black",
returnName = TRUE
)
)
)
),
hr(),
## line plot facet
shinyWidgets::radioGroupButtons(
inputId = "line_plot_separate_by",
label = tags$h4(tags$b("Separate by")),
choices = rlang::set_names(c("none" , "gene_groups") ,
c("None" , "Gene groups")),
individual = T,
justified = T,
status = "success" ,
size = "sm" ,
width = "300px"
),
hr(),
## scale y
conditionalPanel("input.line_plot_separate_by == 'gene_groups'",
shinyWidgets::radioGroupButtons(inputId = "line_plot_facet_scale_free",
label = "Scales" ,
choices = c("Fix" ="fixed" ,
"Free" = "free",
"Free X" ="free_x",
"Free Y" = "free_y"),
selected = "fixed" ,
status = "success" ,size = "sm",
direction = "horizontal",
individual = TRUE ,
justified = T,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
hr()
),
hr(),
## line plot splin shape
sliderInput(inputId = "line_plot_splin_shape" ,
label = tags$h4(tags$b("Line shape")) ,
min = -1,
max = 1,
step = 0.01 ,
value = 0 ,
width = "99%"),
hr(),
## line plot line transparency
sliderInput(inputId = "line_plot_line_transparancy" ,
label = tags$h4(tags$b("Transparency")) ,
min = 0,
max = 1,
step = 0.01 ,
value = 0.5 ,
width = "99%"),
hr(),
## fix number of columns in the facetted ggplot.
numericInput(inputId = "line_plot_ncols",
label = tags$h4(tags$b("Number of columns")),
value = 3 ,
min = 1,
max = 10,
step = 1,
width = "100%"),
hr(),
## line plot point size
sliderInput(inputId = "lineplot_point_size" ,
label = "Point size" ,
min = 1,
max = 10,
value = 2,
step = 0.01),
## line plot line size
sliderInput(inputId = "lineplot_line_size" ,
label = "Line size" ,
min = 1,
max = 10,
value = 2,
step = 0.01)
)
),
## line plot export
column(
width = 3,
export_plot_ui(id = "export_line_plot")
)
)
)
)
),
## line plot data or functional analysis
radioGroupButtons(
inputId = "lineplot_data_or_functional_analysis",
choices = c("Show Data" = "show_lineplot_data",
"Functional Analysis" = "lineplot_functional_analysis"),
status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon")) ,
size = "normal" ,
direction = "horizontal" ,
justified = TRUE , individual = TRUE ,
width = "100%",
selected = ""
),
br(),
## show lineplot data
conditionalPanel(
condition = "input.lineplot_data_or_functional_analysis == 'show_lineplot_data'",
shinyBS::bsCollapse(
open = "Clustered data",
shinyBS::bsCollapsePanel(
title = "Clustered data", style = "primary",
DT::dataTableOutput(outputId = "line_plot_clustred_data", width = "auto") %>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
)
),
## show lineplot functional analysis
conditionalPanel(
condition = "input.lineplot_data_or_functional_analysis == 'lineplot_functional_analysis'",
shinyBS::bsCollapse(
open = "Functional analysis",
shinyBS::bsCollapsePanel(
title = "Functional analysis", style = "primary",
functional_analysis_ui(id = "lineplot_functional_analysis_ui")
)
)
)
),
## triggered action
shinyBS::bsModal(
id = "line_edit_titles", title = "Edit titles", trigger = "trigger_line_edit_titles",
## plot titles
textInput(inputId = "line_plot_title", label = "Plot Title", value = ""),
hr(),
textInput(inputId = "line_x_axis_title", label = "Axis title: X", value = ""),
hr(),
textInput(inputId = "line_y_axis_title", label = "Axis title: Y", value = "value")
)
),
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Heatmap tab panel ----
## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(
title = "Heatmap", value = "heatmap_panel", id = "heatmap_panel",
br(),
fluidRow(
column(
width = 12,
shinyBS::bsCollapse(
open = "Select plot variables",
shinyBS::bsCollapsePanel(
title = "Select plot variables", style = "primary",
column(
width = 12, #style = "overflow-x:auto;",
## select heatmap variables
shinyWidgets::pickerInput(
inputId = "heatmap_vars",
label = "Select sample(s)",
choices = NULL, choicesOpt = F,
selected = "", multiple = T, width = "100%",
options = list(
`actions-box` = TRUE,
size = 10,
`selected-text-format` = "count > 10",
style = "btn-success", `live-search` = TRUE
)
),
## heatmap select gene groups
gene_group_selection_ui(id = "heatmap_select_gene_groups"),
hr(),
## top variable genes to plot in heatmap
shinyWidgets::radioGroupButtons(
inputId = "hm_genes_selection",
label = tags$h4(tags$b("Number of genes to plot")),
choices = c("# top variable genes (By standard deviation)" = "top_variable_genes", "All genes" = "all"),
selected = "top_variable_genes" ,
status = "success" ,
size = "normal",
direction = "horizontal",
justified = T, individual = T ,
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
conditionalPanel(
condition = "input.hm_genes_selection == 'top_variable_genes'",
# heatmap top n genes
numericInput(
inputId = "heatmap_top_n_genes",
label = tags$h4(tags$b("# top variable genes to show")),
value = 500, min = 50, max = 2000, step = 50 #width = "25%"
)
),
hr(),
## heatmap choice for value to use in cluster
fluidRow(
column(
width = 6,
shinyWidgets::radioGroupButtons(
inputId = "heatmap_cluster_value_type",
label = tags$h4(tags$b("Cluster by")),
choices = c("Raw value" = "raw_val" , "Z-Score" = "zscore"),
selected = "zscore",status = "success",
size = "normal",
direction = "horizontal" ,
justified = T , individual = T, width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
## heatmap choice of value to plot
column(
width = 6,
shinyWidgets::radioGroupButtons(
inputId = "heatmap_display_value_type",
label = tags$h4(tags$b("Display value")),
choices = c("Raw value" = "raw" , "Z-Score" = "zscore"),
selected = "zscore",
direction = "horizontal" ,
justified = T ,
individual = T,
width = "100%" , status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
)
),
hr(),
# heat map column row and legend options
fluidRow(
#style = "min-width:1200px",
style = "overflow-x:auto;",
column(
width = 4, style = "min-width:150px",
# heatmap row options
shinyBS::bsCollapse(
open = "Row options",
shinyBS::bsCollapsePanel(
title = "Row options", style = "primary",
## Row names"
shinyWidgets::radioGroupButtons(
inputId = "show_hm_row_names",
label = tags$h4(tags$b("Row names")),
choices = c("TRUE" = TRUE, "FALSE" = FALSE),
selected = FALSE , status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## Font size : Row names
sliderInput(
width = "100%",
inputId = "hm_row_names_font_size",
label = tags$h4(tags$b("Row names font size")),
min = 0.1,
max = 20,
value = 5,
step = 0.1
),
## Adjust height : Rows
# sliderInput(
# width = "100%",
# inputId = "hm_row_height",
# label = tags$h4(tags$b("Row height")),
# min = 0.1,
# max = 50,
# value = 0.1,
# step = 0.1
# ),
## Row clusters
shinyWidgets::radioGroupButtons(
inputId = "heatmap_row_clusters_choices" ,
label = tags$h4(tags$b("Row cluster")),
choices = c("K-means" = "kmeans" , "Gene groups" ="gene_groups"),
selected = "kmeans",
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## of clusters (k-means)
conditionalPanel(condition = "input.heatmap_row_clusters_choices == 'kmeans'",
numericInput(
width = "100%",
inputId = "heatmap_row_nclust",
label = tags$h4(tags$b("# of row clusters (k-means)")),
value = 1,
min = 1,
max = 10,
step = 1
)
),
## row cluster prefix
shiny::textInput(inputId = "hm_cluster_prefix" ,
label = tags$h4(tags$b("Row cluster label prefix")) , value = "Clust_" ,
width = "100%" , placeholder = "Text will appear as row cluster name prefix" ),
# Cluster rows (within the cluster)
shinyWidgets::radioGroupButtons(
inputId = "hm_cluster_rows",
label = tags$h4(tags$b("Row cluster (within the cluster)")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
# # Cluster row slices
# shinyWidgets::radioGroupButtons(
# inputId = "hm_cluster_row_slice",
# label = tags$h4(tags$b("Arrange row cluster slice")),
# choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
# selected = TRUE ,
# status = "success",
# size = "sm",
# direction = "horizontal",
# justified = T,
# individual = T,
# width = "100%",
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
#
## show / hide row dendogram
conditionalPanel(
condition = "input.hm_cluster_rows == 'TRUE'",
shinyWidgets::radioGroupButtons(
inputId = "show_hm_row_dend",
label = tags$h4(tags$b("Row dendogram")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
# show border around cluster
shinyWidgets::radioGroupButtons(
inputId = "hm_border",
label = tags$h4(tags$b("Row cluster border")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## std dev heatmap
shinyWidgets::radioGroupButtons(
inputId = "show_std_dev_hm",
label = tags$h4(tags$b("Add standard deviation heatmap")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## sort by SD heatmap
conditionalPanel(condition = "input.show_std_dev_hm == 'TRUE'" ,
shinyWidgets::radioGroupButtons(
inputId = "sort_hm_by_std_dev",
label = tags$h4(tags$b("Sort by standard deviation")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
)
)
)
),
column(
width = 4, style = "min-width:150px;",
## heatmap column options
shinyBS::bsCollapse(
open = "Column options",
shinyBS::bsCollapsePanel("Column options",
style = "primary",
## heatmap show / hide column names
shinyWidgets::radioGroupButtons(
inputId = "show_hm_colum_names",
label = tags$h4(tags$b("Column names")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = TRUE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## heatmap change font size column names
sliderInput(
inputId = "hm_column_names_font_size",
label = tags$h4(tags$b("Column names font size")),
min = 0.1,
max = 20,
value = 10,
step = 0.1,
width = "100%"
),
# ## adjust column width
# sliderInput(
# inputId = "hm_col_width",
# label = tags$h4(tags$b("Column width")),
# min = 0.1,
# max = 50,
# value = 0.5,
# step = 0.1,
# width = "100%"
# ),
## Column clusters
shinyWidgets::radioGroupButtons(
inputId = "heatmap_column_clusters_choices" ,
label = tags$h4(tags$b("Column cluster")),
choices = c("K-means" = "kmeans" , "Sample groups" ="sample_groups"),
selected = "kmeans",
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## number of column cluster
conditionalPanel(
condition = "input.heatmap_column_clusters_choices == 'kmeans'",
numericInput(
width = "100%",
inputId = "heatmap_coulm_nclust",
label = tags$h4(tags$b("# of column clusters (k-means)")),
value = 1,
min = 1,
max = 10,
step = 1
)
),
## column cluster prefix
shiny::textInput(inputId = "hm_column_cluster_prefix" ,
label = tags$h4(tags$b("Column cluster label prefix")) , value = "Clust_" ,
width = "100%" , placeholder = "Text will appear as column cluster name prefix" ),
## heatmap cluster column with in the cluster
shinyWidgets::radioGroupButtons(
inputId = "hm_cluster_columns",
label = tags$h4(tags$b("Column cluster (within the cluster)")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
# # Cluster column slices
# shinyWidgets::radioGroupButtons(
# inputId = "hm_cluster_column_slice",
# label = tags$h4(tags$b("Arrange column cluster slice")),
# choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
# selected = TRUE ,
# status = "success",
# size = "sm",
# direction = "horizontal",
# justified = T,
# individual = T,
# width = "100%",
# checkIcon = list(
# yes = icon("ok",
# lib = "glyphicon"),
# no = icon("remove",
# lib = "glyphicon"))
# ),
#
## show / hide column dendogram
conditionalPanel("input.hm_cluster_columns == 'TRUE'",
shinyWidgets::radioGroupButtons(
inputId = "show_hm_column_dend",
label = tags$h4(tags$b("Column dendogram")),
choices = c("TRUE" = "TRUE", "FALSE" = "FALSE"),
selected = FALSE ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
)
),
## heatmap top annotations
shinyWidgets::checkboxGroupButtons(
inputId = "heatmap_anno_type",
label = tags$h4(tags$b("Column annotation")),
choices = c("Sample groups" = "show_heatmap_column_groups",
"Boxplot" = "show_heatmap_column_boxplot") ,
status = "success",
size = "sm",
direction = "horizontal",
justified = T,
individual = T,
width = "100%",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## heatmap top annot height
sliderInput(inputId = "heatmap_top_annot_height" ,
label = tags$h4(tags$b("Column annotaion height")) ,
min = 1 , max = 10,
step = 0.05 , value = 1 , width = "100%")
)
)
),
column(
width = 4, style = "min-width:150px;",
# heatmap legend options
shinyBS::bsCollapse(
open = "Legend options",
shinyBS::bsCollapsePanel("Legend options",
style = "primary",
textInput(inputId = "heatmap_legend_name",
label = tags$h4(tags$b("Legend name")),
value = "Value",
width = "100%"),
## heatmap legend position
radioGroupButtons(
width = "100%",
inputId = "heatmap_legend_pos",
label = tags$h4(tags$b("Legend position")),
individual = T,justified = T,
choices = c("T" = "top", "B" = "bottom", "L" = "left", "R" = "right"),
selected = "right",status = "success" ,
size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
## heatmap legend direction
radioGroupButtons(
width = "100%",
inputId = "heatmap_legened_direction",
label = tags$h4(tags$b("Legend direction")),
individual = T,justified = T,
choices = c("H" = "horizontal", "V" = "vertical"),
selected = "vertical",
status = "success" , size = "sm",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon"),
no = icon("remove",
lib = "glyphicon"))
),
br(),
tags$h4(tags$b(("Heatmap Colors"))),
## heatmap color panel
shiny::wellPanel(
## heatmap color : low
colourpicker::colourInput(
inputId = "heatmap_col_low",
label = tags$h4(tags$b("Low")),
value = "#032E80",
returnName = TRUE
),
## heatmap color : med
colourpicker::colourInput(
inputId = "heatmap_col_medium",
label = tags$h4(tags$b("Middle")),
value = "white",
returnName = TRUE
),
## heatmap color : high
colourpicker::colourInput(
inputId = "heatmap_col_high",
label = tags$h4(tags$b("High")),
value = "#910200",
returnName = TRUE
)
),
### set legend minimum
br(),
tags$h4(tags$b(("Heatmap scale"))),
## heatmap scale
wellPanel(
numericInput(inputId = "heatmap_scale_min" ,
label = tags$h4(tags$b("Minimum")),
value = 0),
### set legend maximum
numericInput(inputId = "heatmap_scale_max" ,
label = tags$h4(tags$b("Maximum")) ,
value = 20 )
)
)
)
)
),
hr(),
## generate heatmap submit button.
column(width = 6 , offset = 5,
shinyWidgets::actionBttn(inputId = "generate_heatmap" ,
label = "Plot" ,
icon = icon("ruler-combined") ,
style = "gradient",
color = "success" ,
size = "md",
block = F)
)
)
)
)
)
),
## heatmap plot panel
conditionalPanel(
condition = "input.generate_heatmap && output.heatmap_status == true",
shinyBS::bsCollapse(
open = "Plot",
shinyBS::bsCollapsePanel(
title = "Plot", style = "primary",
fluidRow(style = "overflow-y:auto; max-height:2000px; position:auto;",
column(width = 1), ## empty column
## display heatmap
column(
width = 11,
shinycssloaders::withSpinner(ui_element = plotOutput(outputId = "heatmap",
height = "auto", width = "auto"),
color = "#18BC9C")
),
column(width = 1) ## empty column
),
hr(),
## empty col
column(width = 1),
column(width = 10,
column(width = 6,
## adjust current heatmap height and width
dropdownButton(
inputId = "plot_hm_drop_down",
icon = icon("resize-full", lib = "glyphicon"),
label = "Heatmap browser dimensions",
size = "sm",
circle = F,
status = "success",
up = T,
right = F,
# Adjust height : Rows
sliderInput(
#width = "100%",
inputId = "hm_row_height",
label = tags$h4(tags$b("Row height")),
min = 0.1,
max = 50,
value = 0.1,
step = 0.1
),
## adjust column width
sliderInput(
inputId = "hm_col_width",
label = tags$h4(tags$b("Column width")),
min = 0.1,
max = 50,
value = 0.5,
step = 0.1,
#width = "100%"
)
)
),
column(width = 6,
## export heatmap
export_base_graphics_ui(id = "export_heatmap")
)
), ## empty column
column(width = 1) ## empty column
)
),
## show / hide heatmap data , perform functional analysis , wordcloud.
radioGroupButtons(
inputId = "heatmap_data_or_functional_analysis",
choices = c("Heatmap all data + gene annotation" = "show_heatmap_data",
"Heatmap clusters" = "show_heatmap_clusters",
"Functional analysis" = "heatmap_functional_analysis" ,
"Sample information" = "display_sample_inforamtion"
),
status = "success",
checkIcon = list(
yes = icon("ok",
lib = "glyphicon")) ,
size = "normal" ,
direction = "horizontal" ,justified = TRUE ,
individual = TRUE ,
width = "100%",selected = ""
),
br(),
## display heatmap clusters
conditionalPanel(
condition = "input.heatmap_data_or_functional_analysis == 'show_heatmap_clusters'",
shinyBS::bsCollapse(
open = "Heatmap clusters",
shinyBS::bsCollapsePanel(
title = "Heatmap clusters", style = "primary",
## heatmap cluster side : row or column
div(style="display: inline-block;vertical-align:top; width: 300px;",
shinyWidgets::radioGroupButtons(inputId = "heatmap_cluster_type" ,
label = "Cluster type" ,
choices = c("Row side" = "show_hm_row_side_clusters" ,
"Column side" = "show_hm_column_side_clusters") ,
checkIcon = list(yes = icon("ok",
lib = "glyphicon")),
selected = "show_hm_row_side_clusters" ,
status = "success" ,size = "normal" ,
direction = "horizontal" ,individual = T)
),
## heatmap cluster format : wide or long
div(style="display: inline-block;vertical-align:top; width: 300px;",
shinyWidgets::radioGroupButtons(inputId = "heatmap_cluster_data_format" ,
label = "Data format" ,
choices = c("Wide" = "wide" ,
"Long" = "long") ,
checkIcon = list(yes = icon("ok",
lib = "glyphicon")),
selected = "wide" , status = "success" ,size = "normal" ,
direction = "horizontal" ,individual = T)
),
hr(),
## hm cluster data output
shinycssloaders::withSpinner(
ui_element = DT::dataTableOutput(outputId = "heatmap_display_cluster_data",
width = "auto"),
color = "#18BC9C")
)
)
),
## display heatmap expr mat
conditionalPanel(
condition = "input.heatmap_data_or_functional_analysis == 'show_heatmap_data'",
shinyBS::bsCollapse(
open = "Heatmap all data + gene annotation",
shinyBS::bsCollapsePanel(
title = "Heatmap all data + gene annotation", style = "primary",
DT::dataTableOutput(outputId = "heatmap_data", width = "auto")%>%
shinycssloaders::withSpinner(color = "#18BC9C")
)
)
),
## heatmap functional analysis
conditionalPanel(
condition = "input.heatmap_data_or_functional_analysis == 'heatmap_functional_analysis'",
shinyBS::bsCollapse(
open = "Functional analysis",
shinyBS::bsCollapsePanel(
title = "Functional analysis", style = "primary",
functional_analysis_ui(id = "heatmap_functional_analysis_ui")
)
)
),
## heatmap sample information
conditionalPanel(condition = "input.heatmap_data_or_functional_analysis == 'display_sample_inforamtion' " ,
shinyBS::bsCollapse(
open = "Sample information",
shinyBS::bsCollapsePanel(
title = "Sample information", style = "primary",
fluidRow(
column(
width = 12,
cluster_wise_sample_information_ui("hm_sample_infor")
)
)
)
)
)
)
)
)
)
)
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## About page ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
navbarMenu(title = "About",icon = icon("tag"),
## About page
tabPanel(title = tags$a(icon("searchengin"),
icon = icon("searchengin"),
href = "https://cparsania.github.io/FungiExpresZ/about.html" ,
"Overview",target="_blank")),
# tags$style(HTML("
# section.page-header {
# display: none;
# }
#
# section.main-content{
# max-width: 1000px;
# font-size: 100%;
# }
#
# div#TOC{
# max-width: 1024px;
# font-size: 100%;
# }
# ")),
# includeHTML(system.file("app","rmd_and_html","about.html" , package = "FungiExpresZ"))
# ),
## Video Tutorial page
tabPanel(title = "Video Tutorials", icon = icon("chalkboard-teacher"),
tags$style(HTML("
section.page-header {
display: none;
}
section.main-content{
max-width: 1000px;
font-size: 100%;
}
div#TOC{
max-width: 1024px;
font-size: 100%;
}
")),
includeHTML(system.file("app","rmd_and_html","tutorial.html" , package = "FungiExpresZ"))
),
## Step by step guide page
tabPanel(title = tags$a(icon("paperclip"),
icon = icon("paperclip"),
href = "https://cparsania.github.io/FungiExpresZ/step_by_step_guide.html" ,
"Step-by-step tutorial",target="_blank"))
# tags$style(HTML("
# section.page-header {
# display: none;
# }
#
# section.main-content{
# max-width: 1000px;
# font-size: 100%;
# }
#
# div#TOC{
# max-width: 1024px;
# font-size: 100%;
# }
# ")),
# includeHTML(system.file("app","rmd_and_html","step_by_step_guide.html" , package = "FungiExpresZ"))
# )
#
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Download page ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
navbarMenu(title = "Downloads",
## download GO data
tabPanel("GO data",icon = icon("file-download"),
download_go_data_ui("download_go_data")
),
## download gene expression data
tabPanel("Gene expression data", icon = icon("file-download"),
download_gene_expression_matrix("download_gene_expression_data")
),icon = icon("download") ),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## News & Updates ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(title = "News & Updates", icon = icon("newspaper"),
tags$style(HTML("
section.page-header {
display: none;
}
section.main-content{
max-width: 1000px;
font-size: 100%;
}
div#TOC{
max-width: 1024px;
font-size: 100%;
}
")),
includeHTML(system.file("app","rmd_and_html","newz_and_update.html" , package = "FungiExpresZ"))
#includeHTML("doc/newz_and_update.html")
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## Citations page ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
tabPanel(title = "Citations", icon = icon("stack-exchange"),
tags$style(HTML("
section.page-header {
display: none;
}
section.main-content{
max-width: 1000px;
font-size: 100%;
}
div#TOC{
max-width: 1024px;
font-size: 100%;
}
")),
includeHTML(system.file("app","rmd_and_html","citations.html" , package = "FungiExpresZ"))
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## contact page ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
navbarMenu("Contact",
icon = icon("envelope"),
tabPanel(title = tags$a(icon("github"),href = "https://github.com/cparsania/FungiExpresZ" ,
"GitHub",target="_blank")),
tabPanel(title = tags$a(icon("at"), href = "mailto:chirag.parsania@gmail.com",
"Email")),
tabPanel(title = tags$a(icon("twitter"),href = "https://twitter.com/ChiragParsania" ,
"@ChiragParsania",target="_blank"))
)
),
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
## app footer ----
####@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
hr(),
tags$style(type='text/css', "#app_footer { text-align: center;}"),
tags$div(id = "app_footer",tags$b("FungiExpresZ"), "is developed by ",
tags$a(tags$b("Chirag Parsania ") , icon("twitter") ,
href= "https://twitter.com/ChiragParsania"), "from ",
tags$a(tags$b("Chris Wong's Lab ") , icon("twitter") , href = "https://twitter.com/ChrisKHWong"), "at University of Macau."),
tags$div(id = "app_footer", "For any query or suggestions, please contact",
tags$a(icon("github"),href = "https://github.com/cparsania/FungiExpresZ" ,
"GitHub",target="_blank"),
tags$a(icon("at"), href = "mailto:chirag.parsania@gmail.com",
"Email"),
"."),
br(),
## display latest release
# tags$div(
# style = "text-align:center;",
#
# ),
br(), br(), br(), br(), br(), br(), br(), br()
)
)
}
#' @import shiny
golem_add_external_resources <- function(){
addResourcePath(
'www', system.file('app/www', package = 'FungiExpresZ')
)
tags$head(
golem::activate_js(),
golem::favicon(ico = "www/favicon.ico" , rel = "shortcut icon"),
golem::favicon(ico = "www/apple-touch-icon.png" , rel = "apple-touch-icon"),
golem::favicon(ico = "www/favicon-32x32.png" , rel = "icon"),
golem::favicon(ico = "www/favicon-16x16.png" , rel = "icon"),
golem::favicon(ico = "www/site.webmanifest" , rel = "manifest"),
tags$script(src="www/google_analytics.js")
#tags$html("www/markdown/Tutorial.html"),
#tags$html("www/markdown/newz_and_update.html")
# Add here all the external resources
# If you have a custom.css in the inst/app/www
# Or for example, you can add shinyalert::useShinyalert() here
#tags$link(rel="stylesheet", type="text/css", href="www/custom.css")
#tags$head(includeScript("www/google_analytics.js"))
)
}
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