inst/shiny_old/ui.R
In brentscott93/biophysr: Analysis tools for muscle biophysics
suppressPackageStartupMessages({
library(shiny)
library(shinyFiles)
library(shinyWidgets)
library(shinyjs)
library(shinythemes)
library(colourpicker)
library(shinymanager)
library(shinycssloaders)
library(gtools)
library(gridExtra)
library(pracma)
library(knitr)
library(dygraphs)
library(rmarkdown)
library(plotrix)
library(rhandsontable)
library(RColorBrewer)
library(filesstrings)
library(clipr)
library(biophysr)
library(tidyverse)
library(depmixS4)
})
#start app
ui <- secure_app(head_auth = tags$script(inactivity),
fluidPage(theme = shinytheme("slate"),
useShinyjs(), # Set up shinyjs
# Add a CSS class for white text colour
inlineCSS(list(.white = "background: #FAFAFA")),
navbarPage("biophysr",
tabPanel("Home",
fluidRow(
column(4),
column(4, align = "center",
br(),
br(),
#h1(strong("biophysr")),
#h5("analysis for muscle biophysics"),
br(),
br(),
img(src = "bp3.png"),
br(),
br(),
textOutput("current_user_comment")
#h3("Page is currentlty under construction"),
), # column close
column(4)
) # & fluidrow close
), # home tab panel close
tabPanel("Motility"),
#Mini_ensmble trap Tab
tabPanel("Laser Trap",
fluidRow(column(12,
h2("Laser Trap Analysis")
)#column close
), #row close
fluidRow(column(12,
style = 'border-top: 2px solid grey'
)),
br(),
br(),
fluidRow(column(3,
h4(strong("Tasks"))
),
column(9,
h4(strong("Create and select folders to work in"))
)),
fluidRow( column(3,
radioButtons("trap_tasks_radioButtons", label = NULL,
choices = c("None" = "none",
"Make Observations" = "obs",
"Clean Data" = "clean",
"Analyze" = "analyze",
"Summarize" = "summarize"))
), #columns close
column(3,
style = 'border-left: 1px solid grey',
uiOutput("trap_project"),
conditionalPanel(
condition = "input.trap_project_selectInput == 'create'",
textInput("trap_create_project_textInput", "Name Project"),
actionButton("trap_create_project_actionButton", "Create Project")
)#conditional panel close
), #column close
column(3,
uiOutput("trap_conditions"),
conditionalPanel(
condition = "input.trap_conditions_selectInput == 'create'",
textInput("trap_create_conditions_textInput", "Name Conditions"),
actionButton("trap_create_conditions_actionButton", "Create Conditions")
)#conditional panel close
), #column close
column(3,
uiOutput("trap_date"),
conditionalPanel(
condition = "input.trap_date_selectInput == 'create'",
textInput("trap_create_date_textInput", "Enter Date", placeholder = "6 digits - MMDDYY"),
actionButton("trap_create_date_actionButton", "Create Date")
)#conditional panel close
)#col close
), #fluid row close
fluidRow(column(12,
style = 'border-top: 1px solid grey'
)),
fluidRow(column(12,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'obs'",
h4(strong("Make Trap Observations")))
)),
fluidRow(column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'obs'",
wellPanel(
#h4(strong("Make Trap Observations")),
h5("1) Select Raw Data Files"),
fileInput("trap_txt_upload",
NULL,
multiple = TRUE,
accept = ".txt",
buttonLabel = "Browse...",
placeholder = "Select .txt"),
h5("2) Move raw data to Dropbox"),
actionButton(inputId = "trap_upload",
label = "Upload to Dropbox",
icon = icon("file-upload"),
width = "100%"),
br(),
br(),
h5("3) Choose number of seconds to divide obs by"),
knobInput(inputId = "make_observations_numericInput",
label = NULL,
value = 20,
min = 10,
max = 30),
h5("4) Toggle auto-cal"),
switchInput(inputId = "trap_cal_files",
label = NULL,
value = FALSE,
onStatus = "success",
offStatus = "danger"),
h5("5) Click button to make observations"),
actionButton(inputId = "make_observations_action_button",
label = "Make Observations",
icon = icon("eye"),
width = "100%")
)
)
),
column(9,
plotOutput("trap_cal")
)#col close
),
#row close
fluidRow(
column(12, conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean'",
h4(strong("Clean Data")))
# h3("Toolbar"))#conditional close
)#col close
),#row close
fluidRow(
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean'",
h5("Select Obs"),
uiOutput("trap_obs"))
), #col close
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
h5("Display/Refresh Graph"),
actionButton("trap_clean_show_graph_actionButton",
label ="Graph",
icon = icon("chart-line"),
width = "100%")
)#conditional close
), #col close
column(2,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
h5("File Markers"),
radioButtons("hide_markers",
label = NULL,
choices = c("Show" = "show",
"Hide" = "hide"),
inline = TRUE,
width = "100%")
)#conditional close
), #col close
column(4,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
uiOutput("trap_filter")
) # conditionalclose
) #col close
), #row close
fluidRow(
column(4,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
textOutput("move_files"),
actionButton("trap_move_sheets_actionButton",
"Move",
icon=icon("suitcase"),
width = "100%"),
) #conditional close
), #col close
column(4,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0",
textOutput("trim_files"),
actionButton("trap_trim_dygraph_actionButton",
"Cut",
icon = icon("cut"),
width = "100%")
) #conditional close
), #col close
column(4,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
textOutput("filter_text"),
actionButton("filter_trap_grouped",
label = "Filter",
icon=icon("filter"),
width = "100%")
) #con close
) #col close
), #row close
br(),
fluidRow(
column(12, id = "clean_col",
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 &&
input.trap_clean_show_graph_actionButton != '0'",
br(),
br(),
br(),
dygraphOutput("dygraph_clean") %>% withSpinner(type = 6, color = "#373B38"),
br(),
br(),
br(),
)
)),
br(),
fluidRow(
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_date_selectInput.length > 0",
actionButton("trap_new_directions_actionButton",
"New Directions",
icon = icon('directions'),
width = "100%")
)),
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_date_selectInput.length > 0",
actionButton("trap_save_directions_actionButton",
"Save Directions",
icon = icon("save"),
width = "100%")
)
),
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_date_selectInput.length > 0",
uiOutput("clipboard_copy_from")
)
),
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_date_selectInput.length > 0",
uiOutput("clipboard_copy_to")
)
)
),#row close
br(),
fluidRow(
column(12,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_new_directions_actionButton != 0",
rHandsontableOutput("trap_directions")
)
) #col close
), #row close
br(),
fluidRow(column(3,
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
h3("Analyze")
))),
fluidRow(column(4,
style = 'border-right: 1px solid grey',
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
h4("Run Analysis"),
radioButtons("trap_analyzer",
"Select Analyzer",
choices = c("Mini-Ensemble" = "mini",
"Hidden-Markov" = "hmm"),
inline = TRUE),
radioButtons("trap_cal_choice",
"Select Calibration Method",
choices = c("Auto-cal" = "auto-cal",
"Manual" = "manual"
),
inline = TRUE),
uiOutput("manual_cal_input1"),
uiOutput("manual_cal_input2"),
colourpicker::colourInput("trap_color", label = "Select color", showColour = "both")
) #condition
), #col,
column(4,
# style = 'border-left: 1px solid grey',
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
h4("Quality Check Analysis"),
h5("1) Click button to retrieve analysis results"),
actionButton("get_quality_check_data_actionButton",
"Get Results",
icon = icon("sync-alt")),
br(),
uiOutput("trap_quality_check_obs"),
) #con close
), # columns close
column(4,
style = 'border-left: 1px solid grey',
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
h4("Update Directions"),
h5("Check 'Quality Control' box to accept analysis"),
rHandsontableOutput("update_directions"),
br()
) #con close
) # columns close
), #row close
fluidRow(
column(4,
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
actionButton(inputId = "analyze",
label = "Analyze Trap",
icon = icon("microscope"),
width = "80%")
)
),
column(4,
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
actionButton(inputId = "show_quality_check_graph_actionButton",
label = "Display Results",
icon = icon("chart-line"),
width= "80%")
)
),
column(4,
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
actionButton(inputId = "save_updated_directions",
label = " Save Updated Directions",
icon = icon("save"),
width = "80%")
)
)
), #row close
fluidRow(
column(12,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'analyze' &&
input.trap_date_selectInput != null &&
input.trap_date_selectInput.length > 0 &&
input.show_quality_check_graph_actionButton != '0'",
br(),
br(),
htmlOutput("analysis_report"),
br(),
br()
)
)),
# column(4,
# conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
# h4("Summarize Data"),
# h5("1) Select condition folder to summarize using the folder selector above"),
# h5("2) Choose analyzer that was used"),
# radioButtons(inputId = "summarize_radio_button",
# label = NULL,
# choices = c("Mini-Ensemble", "Hidden-Markov"),
# inline = TRUE),
# h5("3) Click summarize to obtain means and std. errors"),
# actionButton(inputId = "summarize",
# label = "Summarize",
# icon = icon("calculator"))
# ) #con close
# ) # columns close
#), #row close
) #trap tab close
) #navbar page
) #fill/fluid page close
) #secure app close
# END UI
brentscott93/biophysr documentation built on Sept. 14, 2021, 2:35 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
suppressPackageStartupMessages({
library(shiny)
library(shinyFiles)
library(shinyWidgets)
library(shinyjs)
library(shinythemes)
library(colourpicker)
library(shinymanager)
library(shinycssloaders)
library(gtools)
library(gridExtra)
library(pracma)
library(knitr)
library(dygraphs)
library(rmarkdown)
library(plotrix)
library(rhandsontable)
library(RColorBrewer)
library(filesstrings)
library(clipr)
library(biophysr)
library(tidyverse)
library(depmixS4)
})
#start app
ui <- secure_app(head_auth = tags$script(inactivity),
fluidPage(theme = shinytheme("slate"),
useShinyjs(), # Set up shinyjs
# Add a CSS class for white text colour
inlineCSS(list(.white = "background: #FAFAFA")),
navbarPage("biophysr",
tabPanel("Home",
fluidRow(
column(4),
column(4, align = "center",
br(),
br(),
#h1(strong("biophysr")),
#h5("analysis for muscle biophysics"),
br(),
br(),
img(src = "bp3.png"),
br(),
br(),
textOutput("current_user_comment")
#h3("Page is currentlty under construction"),
), # column close
column(4)
) # & fluidrow close
), # home tab panel close
tabPanel("Motility"),
#Mini_ensmble trap Tab
tabPanel("Laser Trap",
fluidRow(column(12,
h2("Laser Trap Analysis")
)#column close
), #row close
fluidRow(column(12,
style = 'border-top: 2px solid grey'
)),
br(),
br(),
fluidRow(column(3,
h4(strong("Tasks"))
),
column(9,
h4(strong("Create and select folders to work in"))
)),
fluidRow( column(3,
radioButtons("trap_tasks_radioButtons", label = NULL,
choices = c("None" = "none",
"Make Observations" = "obs",
"Clean Data" = "clean",
"Analyze" = "analyze",
"Summarize" = "summarize"))
), #columns close
column(3,
style = 'border-left: 1px solid grey',
uiOutput("trap_project"),
conditionalPanel(
condition = "input.trap_project_selectInput == 'create'",
textInput("trap_create_project_textInput", "Name Project"),
actionButton("trap_create_project_actionButton", "Create Project")
)#conditional panel close
), #column close
column(3,
uiOutput("trap_conditions"),
conditionalPanel(
condition = "input.trap_conditions_selectInput == 'create'",
textInput("trap_create_conditions_textInput", "Name Conditions"),
actionButton("trap_create_conditions_actionButton", "Create Conditions")
)#conditional panel close
), #column close
column(3,
uiOutput("trap_date"),
conditionalPanel(
condition = "input.trap_date_selectInput == 'create'",
textInput("trap_create_date_textInput", "Enter Date", placeholder = "6 digits - MMDDYY"),
actionButton("trap_create_date_actionButton", "Create Date")
)#conditional panel close
)#col close
), #fluid row close
fluidRow(column(12,
style = 'border-top: 1px solid grey'
)),
fluidRow(column(12,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'obs'",
h4(strong("Make Trap Observations")))
)),
fluidRow(column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'obs'",
wellPanel(
#h4(strong("Make Trap Observations")),
h5("1) Select Raw Data Files"),
fileInput("trap_txt_upload",
NULL,
multiple = TRUE,
accept = ".txt",
buttonLabel = "Browse...",
placeholder = "Select .txt"),
h5("2) Move raw data to Dropbox"),
actionButton(inputId = "trap_upload",
label = "Upload to Dropbox",
icon = icon("file-upload"),
width = "100%"),
br(),
br(),
h5("3) Choose number of seconds to divide obs by"),
knobInput(inputId = "make_observations_numericInput",
label = NULL,
value = 20,
min = 10,
max = 30),
h5("4) Toggle auto-cal"),
switchInput(inputId = "trap_cal_files",
label = NULL,
value = FALSE,
onStatus = "success",
offStatus = "danger"),
h5("5) Click button to make observations"),
actionButton(inputId = "make_observations_action_button",
label = "Make Observations",
icon = icon("eye"),
width = "100%")
)
)
),
column(9,
plotOutput("trap_cal")
)#col close
),
#row close
fluidRow(
column(12, conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean'",
h4(strong("Clean Data")))
# h3("Toolbar"))#conditional close
)#col close
),#row close
fluidRow(
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean'",
h5("Select Obs"),
uiOutput("trap_obs"))
), #col close
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
h5("Display/Refresh Graph"),
actionButton("trap_clean_show_graph_actionButton",
label ="Graph",
icon = icon("chart-line"),
width = "100%")
)#conditional close
), #col close
column(2,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
h5("File Markers"),
radioButtons("hide_markers",
label = NULL,
choices = c("Show" = "show",
"Hide" = "hide"),
inline = TRUE,
width = "100%")
)#conditional close
), #col close
column(4,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
uiOutput("trap_filter")
) # conditionalclose
) #col close
), #row close
fluidRow(
column(4,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
textOutput("move_files"),
actionButton("trap_move_sheets_actionButton",
"Move",
icon=icon("suitcase"),
width = "100%"),
) #conditional close
), #col close
column(4,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0",
textOutput("trim_files"),
actionButton("trap_trim_dygraph_actionButton",
"Cut",
icon = icon("cut"),
width = "100%")
) #conditional close
), #col close
column(4,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 ",
textOutput("filter_text"),
actionButton("filter_trap_grouped",
label = "Filter",
icon=icon("filter"),
width = "100%")
) #con close
) #col close
), #row close
br(),
fluidRow(
column(12, id = "clean_col",
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_obs_selectInput != null &&
input.trap_obs_selectInput.length > 0 &&
input.trap_clean_show_graph_actionButton != '0'",
br(),
br(),
br(),
dygraphOutput("dygraph_clean") %>% withSpinner(type = 6, color = "#373B38"),
br(),
br(),
br(),
)
)),
br(),
fluidRow(
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_date_selectInput.length > 0",
actionButton("trap_new_directions_actionButton",
"New Directions",
icon = icon('directions'),
width = "100%")
)),
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_date_selectInput.length > 0",
actionButton("trap_save_directions_actionButton",
"Save Directions",
icon = icon("save"),
width = "100%")
)
),
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_date_selectInput.length > 0",
uiOutput("clipboard_copy_from")
)
),
column(3,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_date_selectInput.length > 0",
uiOutput("clipboard_copy_to")
)
)
),#row close
br(),
fluidRow(
column(12,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'clean' &&
input.trap_new_directions_actionButton != 0",
rHandsontableOutput("trap_directions")
)
) #col close
), #row close
br(),
fluidRow(column(3,
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
h3("Analyze")
))),
fluidRow(column(4,
style = 'border-right: 1px solid grey',
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
h4("Run Analysis"),
radioButtons("trap_analyzer",
"Select Analyzer",
choices = c("Mini-Ensemble" = "mini",
"Hidden-Markov" = "hmm"),
inline = TRUE),
radioButtons("trap_cal_choice",
"Select Calibration Method",
choices = c("Auto-cal" = "auto-cal",
"Manual" = "manual"
),
inline = TRUE),
uiOutput("manual_cal_input1"),
uiOutput("manual_cal_input2"),
colourpicker::colourInput("trap_color", label = "Select color", showColour = "both")
) #condition
), #col,
column(4,
# style = 'border-left: 1px solid grey',
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
h4("Quality Check Analysis"),
h5("1) Click button to retrieve analysis results"),
actionButton("get_quality_check_data_actionButton",
"Get Results",
icon = icon("sync-alt")),
br(),
uiOutput("trap_quality_check_obs"),
) #con close
), # columns close
column(4,
style = 'border-left: 1px solid grey',
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
h4("Update Directions"),
h5("Check 'Quality Control' box to accept analysis"),
rHandsontableOutput("update_directions"),
br()
) #con close
) # columns close
), #row close
fluidRow(
column(4,
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
actionButton(inputId = "analyze",
label = "Analyze Trap",
icon = icon("microscope"),
width = "80%")
)
),
column(4,
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
actionButton(inputId = "show_quality_check_graph_actionButton",
label = "Display Results",
icon = icon("chart-line"),
width= "80%")
)
),
column(4,
conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
actionButton(inputId = "save_updated_directions",
label = " Save Updated Directions",
icon = icon("save"),
width = "80%")
)
)
), #row close
fluidRow(
column(12,
conditionalPanel(
condition = "input.trap_tasks_radioButtons == 'analyze' &&
input.trap_date_selectInput != null &&
input.trap_date_selectInput.length > 0 &&
input.show_quality_check_graph_actionButton != '0'",
br(),
br(),
htmlOutput("analysis_report"),
br(),
br()
)
)),
# column(4,
# conditionalPanel(condition = "input.trap_tasks_radioButtons == 'analyze'",
# h4("Summarize Data"),
# h5("1) Select condition folder to summarize using the folder selector above"),
# h5("2) Choose analyzer that was used"),
# radioButtons(inputId = "summarize_radio_button",
# label = NULL,
# choices = c("Mini-Ensemble", "Hidden-Markov"),
# inline = TRUE),
# h5("3) Click summarize to obtain means and std. errors"),
# actionButton(inputId = "summarize",
# label = "Summarize",
# icon = icon("calculator"))
# ) #con close
# ) # columns close
#), #row close
) #trap tab close
) #navbar page
) #fill/fluid page close
) #secure app close
# END UI
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