inst/shiny-app/ui.R
In wrightrc/r1001genomes: Access and analyze the 1001 genomes Arabidopsis resequencing dataset
library(leaflet)
library(shinyBS)
library(shinythemes)
library(knitr)
library(ggplot2)
ui <- function(request){ fluidPage(
theme = shinytheme(theme = "flatly"),
#### Header ####
tags$head(
# Custom CSS code
tags$link(rel = "stylesheet", type = "text/css", href = "simple_blue_theme.css"),
tags$link(rel = "stylesheet", type = "text/css", href = "general.css")
),
titlePanel(
tags$div(class= "title-panel",
"Arabidopsis Natural Variation Webtool"
)
),
"This app provides an interface to examine the natural variation of specified genes of interest in the 1001 Genomes project dataset. To save or share a state of this app, use the bookmark button.", HTML("</br>"),
bookmarkButton(),
tags$h5('style'="color:red", "This app is currently a work in progress."),
# themeSelector(),
tags$br(),
bsCollapse(id = "collapse 1", multiple=TRUE, open=c("Gene Select"),
bsCollapsePanel(
title=tagList("Gene Select", tags$h6(style= "display:inline", "(click to expand/collapse)")),
value="Gene Select",
fluidRow(
column(5,
tags$h3("Select Genes"),
tags$h5("Type a list of gene loci in the box below, separated by commas. "),
textAreaInput(inputId = "gene_ids", label = NULL,
width = "375px", height = 75, value = "AT3G62980, AT3G26810"),
checkboxInput("STATS_quick_demo", label="Quick Demo"),
actionButton(inputId="STATS_submit", label = "Submit")
),
column(2, align="center", tags$h3("OR")),
column(5,
tags$h3("Upload File"),
tags$h5("browse to a .csv file containing 'tair_locus' and 'name' fields.
The name field should be the TAIR symbol or moniker you would like to identify your genes by."),
fileInput("genesFile", label=NULL),
actionButton(inputId="file_submit", label = "Submit")
)
)
),
bsCollapsePanel(
title=tagList("Annotation Files", tags$h6(style= "display:inline", "(click to expand/collapse)")),
value="Annotation Files",
fluidRow(
column(5,
tags$h3("Upload an annotation file"),
tags$h5("Browse to a '.csv' file containing a 'gene' field matching the tair loci or gene symbols of your genes of interest.
Or create a new annotation file by downloading the empty template file and adding annotations to it.")
),
column(4,
fileInput("annoFile", label="Upload Annotation File:"),
tags$h5(tags$strong("Download Empty Annotation File Template:")),
downloadButton("annoTemplateDownload",label="Download Template")
),
column(3,
tags$h5(tags$strong("Submit Uploaded Annotation File:")),
actionButton(inputId="annoSubmit", label = "Submit")
)
)
)
),
tags$br(),
tags$div(class="navbar-margin",navbarPage(title="TABS:",
tabPanel("SNP Stats",
## Tab 1 ###############################################################
tags$div(class="output-format",
tags$h3("Gene Information"),
tags$h5("This table provides details on the gene(s) input above, including transcript IDs and chromosomal locations."),
downloadButton("tab1.downloadGeneInfo","Download Content of Table Below"),
DT::dataTableOutput("tab1.genes_table")
),
tags$br(),
tags$div(class="output-format",
tags$h3("Summary of Sequence Diversity"),
downloadButton("tab1.downloadStats","Download Content of Tables Below"),
tags$h4("Total Polymorphism Counts"),
HTML("<h5>
This table provides counts of the total, non-unique polymorphisms present in the given genes by gene structure. These numbers can be quite high if the reference (Col-0) has a minor allele. \"coding_total\" is the sum of missense, nonsense and synonymous variants.
</h5>"),
DT::dataTableOutput("tab1.SNPcounts"),
tags$hr(),
tags$h4("Unique Allele Counts"),
HTML("<h5>
This table provides counts of unique alleles by gene structure.
</h5>"),
DT::dataTableOutput("tab1.SNPcountsUnique"),
tags$hr(),
tags$h4("Nucleotide Diversity Statistics"),
HTML("<h5>
This table provides for each given gene the nucleotide diversity as Nei and Li's <i>π</i> (the average number of nucleotide differences per site between all possible pairs of sequence) at synonymous (<i>π<sub>S</sub></i>) and nonsynonymous (<i>π<sub>N</sub></i>) sites.
</br>
In the future we plan to add
Fixation index (<i>F<sub>ST</sub></i>),
Tajima's <i>D</i> and
Watterson's <i>θ</i> to this table."),
DT::dataTableOutput("tab1.Diversity_table")
)
),
## Tab 2 - Diversity Plot #####################################################
tabPanel("Diversity Plot",
#tags$br(),
tags$div(class="input-format",
tags$h3("Select a Gene"),
tags$h5("Select a transcript ID in the box below"),
uiOutput("tab2.selectGene")
),
tags$hr(),
tags$div(class="output-format",
tags$h3("Selected Gene Information"),
DT::dataTableOutput("tab2.gene_table")
),
tags$br(),
tags$div(class="output-format",
tags$h3("Plot of Nucleotide Diversity Statistic by Codon"),
tags$h5("To see details on specific points, click and drag to create a box selecting points."),
tags$div(style = "position:relative",
plotOutput("diversityPlot", brush="plot_brush", hover = hoverOpts("div_plot_hover", delay = 100,
delayType = "debounce"), height = 400),
uiOutput("tab2.hover")
),
verbatimTextOutput("info")
),
tags$br(),
tags$div(class="output-format",
tags$h3("Diversity Plot Data"),
tags$h5("This table provides the raw data from the plot. \"POS\" is the chromosomal position of the SNP,
the Amino_Acid_Change field provides both the amino acid as well as the base change"),
downloadButton("tab2.downloadSNPData","Download Content of Table Below"),
DT::dataTableOutput("Diversity_Table")
)
),
## Tab 3 - SNP Mapping #######################################################
tabPanel("SNP Mapping",
#tags$br(),
tags$div(class="input-format",
tags$h3("Select Genes and Filter Diversity Parameter"),
tags$h5("Select one or more transcript IDs below and use the slider to select a minimum sitewise nucleotide diversity"),
# textInput(inputId="tab3.Gene", label=NULL,
# value="AT1G80490"),
uiOutput("tab3.selectGene"),
# actionButton(inputId="tab3.Submit", label="Submit"),
sliderInput(inputId="tab3.filter_value", label="Log Nucleotide diversity filter limit",
min=-4, max=0, value=c(-3, -1), step=0.05),
radioButtons("tab3.SNPtype", "Type of SNP to mark",
choices=c("All", "Coding", "Missense"))
# verbatimTextOutput("tab3.debug")
),
tags$br(),
uiOutput("tab3.mutation_checkbox"),
tags$hr(),
tags$div(class="output-format",
tags$h3("Accession Map"),
tags$h5("Zoom with scroll wheel, click and drag to pan, click on individual point to see details.
Use the layers pop-out to the lower left of the map to hide or show sets of accessions with the same variant."),
leafletOutput("tab3.map", width = "95%")
),
tags$br(),
tags$div(class="output-format",
tags$h3("Map Data"),
downloadButton("tab3.downloadMapData","Download Content of Table Below"),
DT::dataTableOutput("tab3.dataTable")
)
),
## Tab 4 #########################################################
tabPanel("SNP Browser",
#tags$br(),
tags$div(class="input-format",
tags$h3("Gene Select"),
tags$h5("select one or more transcipt IDs below"),
uiOutput("tab4.selectGene")
),
tags$br(),
tags$div(class="input-format",
tags$h3("Filters"),
tags$h5("NOTE: all filters are combined by a logical AND.
So for a row to be displayed, it must satisfy the requirements of ALL the filters."),
checkboxInput("tab4.filterRef", "hide 0|0 genotypes?", FALSE),
#### Filter 1 ####
wellPanel(fluidRow(
column(2,tags$h4("Filter 1")),
column(3,
selectInput("tab4.filter1.column", label="column select",
choices=filterTab.allCols)
),
column(5,
textInput("tab4.filter1.textIn", "values to match")
),
column(2,
tags$h5("Separate values with a comma followed by a space \n(ie. \"a, b\"). ")
)
)),
#### Filter 2 ####
wellPanel(fluidRow(
column(2, tags$h4("Filter 2")),
column(3,
selectInput("tab4.filter2.column", label="column select",
choices=filterTab.allCols)
),
column(5,
textInput("tab4.filter2.textIn", "values to match")
),
column(2,
tags$h5("Separate values with a comma followed by a space \n(ie. \"a, b\"). ")
)
)),
#### filter 3 ####
wellPanel(fluidRow(
column(2, tags$h4("Filter 3"),tags$h4("(Numeric)")),
column(3,
selectInput("tab4.filter3.column", label="column select",
choices=filterTab.numericCols)
),
column(2, numericInput("tab4.filter3.min", "MIN", NA)),
column(2, numericInput("tab4.filter3.max", "MAX", NA)),
column(3,
checkboxInput("tab4.filter3.missing", "keep rows with missing values?")
)
)),
#### Filter 4 ####
wellPanel(fluidRow(
column(2, tags$h4("Filter 4"),tags$h4("(Numeric)")),
column(3,
selectInput("tab4.filter4.column", label="column select",
choices=filterTab.numericCols)
),
column(2, numericInput("tab4.filter4.min", "MIN", NA)),
column(2, numericInput("tab4.filter4.max", "MAX", NA)),
column(3,
checkboxInput("tab4.filter4.missing", "keep rows with missing values?")
)
)),
actionButton(inputId="tab4.updateFilter", label = "Apply Filters")
),
tags$hr(),
# verbatimTextOutput("tab4.debug"), un-comment to debug
tags$div(class="output-format",
tags$h3("Filtered Variants"),
tags$h5("This table provides ..."),
downloadButton("tab4.downloadVariantTable","Download Content of Table Below"),
DT::dataTableOutput("tab4.variantTable")
)
),
## Tab 5 - Alignments #########################################################
tabPanel("Alignments",
#tags$br(),
tags$div(class="input-format",
tags$h3("Select Genes and Type"),
tags$h5("Select one or more transcript IDs below and the type of alignment to show"),
uiOutput("tab5.selectGene")
),
tags$br(),
tags$div(class = "output-format",
tags$h3("Sequence Alignment"),
tags$h5("Alignment made with",tags$a(href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0749-z", target = "_blank", "DECIPHER"), ". The x-axis is the position within the alignment. Hover over the alignment to see details (ggplot2 tooltip by", tags$a(href = "https://gitlab.com/snippets/16220", target = "_blank", "Pawel"), ". 'seq_pos' is the position in the sequence with name 'seq_name' of the type chosen above."),
tags$div(
style = "position:relative",
uiOutput("plot.ui"),
uiOutput("aln_plot_hover")),
plotOutput('tab5.aln_plot_legend', height = "200px")
),
# verbatimTextOutput("event")
tags$br()#,
#tags$h5("Click and drag to pan. Made with", tags$a(href="https://zachcp.github.io/msaR/", "msaR")),
#msaROutput(outputId = "tab5.alignment"), height = "auto")
# Remove DECIPHER BrowseSeqs
# but perhaps the side scrolling div will come in handy again
# tags$div(class = "wrapper",
# tags$div(class = "scrolls",
# htmlOutput("tab5.BrowseSeqs", inline = TRUE)
# )
# ),
),
tabPanel("About",
## About Tab ######################################################
#tags$br(),
column(6,
tags$div(class="output-format",
includeHTML("Glossary.html")
)
),
column(6,
tags$div(class="output-format",
includeHTML("Bibliography.html")
)
)
)
)) #end of tabset panel
# "THIS IS THE FOOTER"
)}
wrightrc/r1001genomes documentation built on Nov. 10, 2019, 12:45 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(leaflet)
library(shinyBS)
library(shinythemes)
library(knitr)
library(ggplot2)
ui <- function(request){ fluidPage(
theme = shinytheme(theme = "flatly"),
#### Header ####
tags$head(
# Custom CSS code
tags$link(rel = "stylesheet", type = "text/css", href = "simple_blue_theme.css"),
tags$link(rel = "stylesheet", type = "text/css", href = "general.css")
),
titlePanel(
tags$div(class= "title-panel",
"Arabidopsis Natural Variation Webtool"
)
),
"This app provides an interface to examine the natural variation of specified genes of interest in the 1001 Genomes project dataset. To save or share a state of this app, use the bookmark button.", HTML("</br>"),
bookmarkButton(),
tags$h5('style'="color:red", "This app is currently a work in progress."),
# themeSelector(),
tags$br(),
bsCollapse(id = "collapse 1", multiple=TRUE, open=c("Gene Select"),
bsCollapsePanel(
title=tagList("Gene Select", tags$h6(style= "display:inline", "(click to expand/collapse)")),
value="Gene Select",
fluidRow(
column(5,
tags$h3("Select Genes"),
tags$h5("Type a list of gene loci in the box below, separated by commas. "),
textAreaInput(inputId = "gene_ids", label = NULL,
width = "375px", height = 75, value = "AT3G62980, AT3G26810"),
checkboxInput("STATS_quick_demo", label="Quick Demo"),
actionButton(inputId="STATS_submit", label = "Submit")
),
column(2, align="center", tags$h3("OR")),
column(5,
tags$h3("Upload File"),
tags$h5("browse to a .csv file containing 'tair_locus' and 'name' fields.
The name field should be the TAIR symbol or moniker you would like to identify your genes by."),
fileInput("genesFile", label=NULL),
actionButton(inputId="file_submit", label = "Submit")
)
)
),
bsCollapsePanel(
title=tagList("Annotation Files", tags$h6(style= "display:inline", "(click to expand/collapse)")),
value="Annotation Files",
fluidRow(
column(5,
tags$h3("Upload an annotation file"),
tags$h5("Browse to a '.csv' file containing a 'gene' field matching the tair loci or gene symbols of your genes of interest.
Or create a new annotation file by downloading the empty template file and adding annotations to it.")
),
column(4,
fileInput("annoFile", label="Upload Annotation File:"),
tags$h5(tags$strong("Download Empty Annotation File Template:")),
downloadButton("annoTemplateDownload",label="Download Template")
),
column(3,
tags$h5(tags$strong("Submit Uploaded Annotation File:")),
actionButton(inputId="annoSubmit", label = "Submit")
)
)
)
),
tags$br(),
tags$div(class="navbar-margin",navbarPage(title="TABS:",
tabPanel("SNP Stats",
## Tab 1 ###############################################################
tags$div(class="output-format",
tags$h3("Gene Information"),
tags$h5("This table provides details on the gene(s) input above, including transcript IDs and chromosomal locations."),
downloadButton("tab1.downloadGeneInfo","Download Content of Table Below"),
DT::dataTableOutput("tab1.genes_table")
),
tags$br(),
tags$div(class="output-format",
tags$h3("Summary of Sequence Diversity"),
downloadButton("tab1.downloadStats","Download Content of Tables Below"),
tags$h4("Total Polymorphism Counts"),
HTML("<h5>
This table provides counts of the total, non-unique polymorphisms present in the given genes by gene structure. These numbers can be quite high if the reference (Col-0) has a minor allele. \"coding_total\" is the sum of missense, nonsense and synonymous variants.
</h5>"),
DT::dataTableOutput("tab1.SNPcounts"),
tags$hr(),
tags$h4("Unique Allele Counts"),
HTML("<h5>
This table provides counts of unique alleles by gene structure.
</h5>"),
DT::dataTableOutput("tab1.SNPcountsUnique"),
tags$hr(),
tags$h4("Nucleotide Diversity Statistics"),
HTML("<h5>
This table provides for each given gene the nucleotide diversity as Nei and Li's <i>π</i> (the average number of nucleotide differences per site between all possible pairs of sequence) at synonymous (<i>π<sub>S</sub></i>) and nonsynonymous (<i>π<sub>N</sub></i>) sites.
</br>
In the future we plan to add
Fixation index (<i>F<sub>ST</sub></i>),
Tajima's <i>D</i> and
Watterson's <i>θ</i> to this table."),
DT::dataTableOutput("tab1.Diversity_table")
)
),
## Tab 2 - Diversity Plot #####################################################
tabPanel("Diversity Plot",
#tags$br(),
tags$div(class="input-format",
tags$h3("Select a Gene"),
tags$h5("Select a transcript ID in the box below"),
uiOutput("tab2.selectGene")
),
tags$hr(),
tags$div(class="output-format",
tags$h3("Selected Gene Information"),
DT::dataTableOutput("tab2.gene_table")
),
tags$br(),
tags$div(class="output-format",
tags$h3("Plot of Nucleotide Diversity Statistic by Codon"),
tags$h5("To see details on specific points, click and drag to create a box selecting points."),
tags$div(style = "position:relative",
plotOutput("diversityPlot", brush="plot_brush", hover = hoverOpts("div_plot_hover", delay = 100,
delayType = "debounce"), height = 400),
uiOutput("tab2.hover")
),
verbatimTextOutput("info")
),
tags$br(),
tags$div(class="output-format",
tags$h3("Diversity Plot Data"),
tags$h5("This table provides the raw data from the plot. \"POS\" is the chromosomal position of the SNP,
the Amino_Acid_Change field provides both the amino acid as well as the base change"),
downloadButton("tab2.downloadSNPData","Download Content of Table Below"),
DT::dataTableOutput("Diversity_Table")
)
),
## Tab 3 - SNP Mapping #######################################################
tabPanel("SNP Mapping",
#tags$br(),
tags$div(class="input-format",
tags$h3("Select Genes and Filter Diversity Parameter"),
tags$h5("Select one or more transcript IDs below and use the slider to select a minimum sitewise nucleotide diversity"),
# textInput(inputId="tab3.Gene", label=NULL,
# value="AT1G80490"),
uiOutput("tab3.selectGene"),
# actionButton(inputId="tab3.Submit", label="Submit"),
sliderInput(inputId="tab3.filter_value", label="Log Nucleotide diversity filter limit",
min=-4, max=0, value=c(-3, -1), step=0.05),
radioButtons("tab3.SNPtype", "Type of SNP to mark",
choices=c("All", "Coding", "Missense"))
# verbatimTextOutput("tab3.debug")
),
tags$br(),
uiOutput("tab3.mutation_checkbox"),
tags$hr(),
tags$div(class="output-format",
tags$h3("Accession Map"),
tags$h5("Zoom with scroll wheel, click and drag to pan, click on individual point to see details.
Use the layers pop-out to the lower left of the map to hide or show sets of accessions with the same variant."),
leafletOutput("tab3.map", width = "95%")
),
tags$br(),
tags$div(class="output-format",
tags$h3("Map Data"),
downloadButton("tab3.downloadMapData","Download Content of Table Below"),
DT::dataTableOutput("tab3.dataTable")
)
),
## Tab 4 #########################################################
tabPanel("SNP Browser",
#tags$br(),
tags$div(class="input-format",
tags$h3("Gene Select"),
tags$h5("select one or more transcipt IDs below"),
uiOutput("tab4.selectGene")
),
tags$br(),
tags$div(class="input-format",
tags$h3("Filters"),
tags$h5("NOTE: all filters are combined by a logical AND.
So for a row to be displayed, it must satisfy the requirements of ALL the filters."),
checkboxInput("tab4.filterRef", "hide 0|0 genotypes?", FALSE),
#### Filter 1 ####
wellPanel(fluidRow(
column(2,tags$h4("Filter 1")),
column(3,
selectInput("tab4.filter1.column", label="column select",
choices=filterTab.allCols)
),
column(5,
textInput("tab4.filter1.textIn", "values to match")
),
column(2,
tags$h5("Separate values with a comma followed by a space \n(ie. \"a, b\"). ")
)
)),
#### Filter 2 ####
wellPanel(fluidRow(
column(2, tags$h4("Filter 2")),
column(3,
selectInput("tab4.filter2.column", label="column select",
choices=filterTab.allCols)
),
column(5,
textInput("tab4.filter2.textIn", "values to match")
),
column(2,
tags$h5("Separate values with a comma followed by a space \n(ie. \"a, b\"). ")
)
)),
#### filter 3 ####
wellPanel(fluidRow(
column(2, tags$h4("Filter 3"),tags$h4("(Numeric)")),
column(3,
selectInput("tab4.filter3.column", label="column select",
choices=filterTab.numericCols)
),
column(2, numericInput("tab4.filter3.min", "MIN", NA)),
column(2, numericInput("tab4.filter3.max", "MAX", NA)),
column(3,
checkboxInput("tab4.filter3.missing", "keep rows with missing values?")
)
)),
#### Filter 4 ####
wellPanel(fluidRow(
column(2, tags$h4("Filter 4"),tags$h4("(Numeric)")),
column(3,
selectInput("tab4.filter4.column", label="column select",
choices=filterTab.numericCols)
),
column(2, numericInput("tab4.filter4.min", "MIN", NA)),
column(2, numericInput("tab4.filter4.max", "MAX", NA)),
column(3,
checkboxInput("tab4.filter4.missing", "keep rows with missing values?")
)
)),
actionButton(inputId="tab4.updateFilter", label = "Apply Filters")
),
tags$hr(),
# verbatimTextOutput("tab4.debug"), un-comment to debug
tags$div(class="output-format",
tags$h3("Filtered Variants"),
tags$h5("This table provides ..."),
downloadButton("tab4.downloadVariantTable","Download Content of Table Below"),
DT::dataTableOutput("tab4.variantTable")
)
),
## Tab 5 - Alignments #########################################################
tabPanel("Alignments",
#tags$br(),
tags$div(class="input-format",
tags$h3("Select Genes and Type"),
tags$h5("Select one or more transcript IDs below and the type of alignment to show"),
uiOutput("tab5.selectGene")
),
tags$br(),
tags$div(class = "output-format",
tags$h3("Sequence Alignment"),
tags$h5("Alignment made with",tags$a(href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0749-z", target = "_blank", "DECIPHER"), ". The x-axis is the position within the alignment. Hover over the alignment to see details (ggplot2 tooltip by", tags$a(href = "https://gitlab.com/snippets/16220", target = "_blank", "Pawel"), ". 'seq_pos' is the position in the sequence with name 'seq_name' of the type chosen above."),
tags$div(
style = "position:relative",
uiOutput("plot.ui"),
uiOutput("aln_plot_hover")),
plotOutput('tab5.aln_plot_legend', height = "200px")
),
# verbatimTextOutput("event")
tags$br()#,
#tags$h5("Click and drag to pan. Made with", tags$a(href="https://zachcp.github.io/msaR/", "msaR")),
#msaROutput(outputId = "tab5.alignment"), height = "auto")
# Remove DECIPHER BrowseSeqs
# but perhaps the side scrolling div will come in handy again
# tags$div(class = "wrapper",
# tags$div(class = "scrolls",
# htmlOutput("tab5.BrowseSeqs", inline = TRUE)
# )
# ),
),
tabPanel("About",
## About Tab ######################################################
#tags$br(),
column(6,
tags$div(class="output-format",
includeHTML("Glossary.html")
)
),
column(6,
tags$div(class="output-format",
includeHTML("Bibliography.html")
)
)
)
)) #end of tabset panel
# "THIS IS THE FOOTER"
)}
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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