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app.R
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app.R
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# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# VolcaNoseR - A Shiny app for for nosing around in volcano plots
# Created by Joachim Goedhart (@joachimgoedhart), first version 2019
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# Joachim Goedhart (C) 2019
# electronic mail address: j #dot# goedhart #at# uva #dot# nl
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# Allow files up to 10 Mb
options(shiny.maxRequestSize=10*1024^2)
#Load necessary packages
library(shiny)
library(tidyverse)
library(ggrepel)
library(shinycssloaders)
library(DT)
library(RCurl)
library(ggiraph)
library(htmlwidgets)
source("themes.R")
#df_example <- read.csv("Data-Vulcano-plot.csv", na.strings = "")
df_example_cdc42 <- read.csv("elife-45916-Cdc42QL_data.csv", na.strings = "")
df_example_diffgenes_HFHC <- read.csv("Becares-diffgenes_HFHC.csv", na.strings = "")
#From Color Universal Design (CUD): https://jfly.uni-koeln.de/color/
Okabe_Ito <- c("#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7", "#000000")
# Create a reactive object here that we can share between all the sessions.
vals <- reactiveValues(count=0)
# Define UI
ui <- fluidPage(
#Required for proper formatting of the font of the girafeOutput
tags$head(tags$style(type="text/css", "text {font-family: sans-serif}")),
# Application title
titlePanel("VolcaNoseR - Exploring volcano plots"),
# Sidebar with a slider input for number of bins
sidebarLayout(
sidebarPanel(width=3,
conditionalPanel(
condition = "input.tabs=='Plot' || input.tabs=='iPlot'",
# h3("Select Geom(etry)"),
# selectInput("geom", label = NULL, choices = list("geom_point"="geom_point", "-"="-")),
# conditionalPanel(condition = "input.geom=='geom_line'",
# selectInput('grouping', label="Group", choices = list("-"="-"), selected = "-")
# ),
h4("Aesthetics"),
sliderInput("pointSize", "Size of the datapoints", 0, 10, 4),
sliderInput("alphaInput", "Visibility of the data", 0, 1, 0.8),
# hr(),
h4("Selection & Annotation of hits"),
textInput("fc_cutoff", "Fold Change threshold (min,max):", value = "-1.5,1.5"),
numericInput("p_cutoff", "Significance threshold:", value = 2),
selectInput("direction", label="Use thresholds to filter hits:", choices = list("Ignore thresholds"="all", "Changed (and significant)"="significant","Increased (and significant)"="increased", "Decreased (and significant)"="decreased"), selected ="significant"),
selectInput("criterion", label="Criterion for ranking hits:", choices = list("Manhattan distance"="manh", "Euclidean distance"="euclid","Fold change"="fc","Significance"="sig"), selected ="manh"),
numericInput("top_x", "Number of top hits (0 to hide):", value = 10),
# textInput("user_gene_list2", "Selected hits (names separated by commas, e.g. DOK6,TBX5)", value = ""),
selectizeInput(inputId = 'user_gene_list',
label = "User selected hits:",
choices = "-",
selected = "-",
multiple = TRUE, # allow for multiple inputs
options = list(create = TRUE)), # if TRUE, allows newly created inputs
checkboxInput(inputId = "show_table",
label = "Show table with hits",
value = FALSE),
checkboxInput(inputId = "hide_labels",
label = "Hide labels in the plot",
value = FALSE),
radioButtons("adjustcolors", "Color (Unchanged,Incr.,Decr.,User selected)", choices =
list(
"Grey, Red, Blue, Black" = 1,
"Grey, Blue, Green, Black" = 3,
"Grey, Cyan, Purple, Black" = 4,
"User defined"=5),
selected = 1),
conditionalPanel(condition = "input.adjustcolors == 5",
textInput("user_color_list", "List of names or hexadecimal codes", value = "turquoise2,#FF2222,lawngreen,orange")),
checkboxInput(inputId = "dark", label = "Dark Theme", value = FALSE),
# h5("",
# a("Click here for more info on color names",
# href = "http://www.endmemo.com/program/R/color.php", target="_blank"))
h4("Transformation & Scaling"),
# conditionalPanel(condition = "input.transform==true",
#
# radioButtons(
# "transform_x", "Transform x-axis data:",
# choices =
# list("No" = "No",
# "log2" = "log2",
# "log10" = "log10",
# "-log10" = "minus_log10"),
# selected = "No"),
# radioButtons(
# "transform_y", "Transform y-axis data:",
# choices =
# list("No" = "No",
# "log2" = "log2",
# "log10" = "log10",
# "-log10" = "minus_log10"),
# selected = "No")
#
#
# ),
checkboxInput(inputId = "rotate_plot",
label = "Rotate plot 90 degrees",
value = FALSE),
checkboxInput(inputId = "add_grid",
label = "Add gridlines",
value = FALSE),
checkboxInput(inputId = "change_scale",
label = "Change scale",
value = FALSE),
conditionalPanel(
condition = "input.change_scale == true",
textInput("range_x", "Range x-axis (min,max)", value = "")
),
conditionalPanel(
condition = "input.change_scale == true",
textInput("range_y", "Range y-axis (min,max)", value = ""),
checkboxInput(inputId = "scale_log_10", label = "Log10 scale on y-axis", value = FALSE)
),
numericInput("plot_height", "Plot height (# pixels): ", value = 600),
numericInput("plot_width", "Plot width (# pixels):", value = 800),
h4("Labels"),
checkboxInput(inputId = "add_title",
label = "Add title",
value = FALSE),
conditionalPanel(
condition = "input.add_title == true",
textInput("title", "Title:", value = "")
),
checkboxInput(inputId = "label_axes",
label = "Change axis labels",
value = FALSE),
conditionalPanel(
condition = "input.label_axes == true",
textInput("lab_x", "X-axis:", value = ""),
textInput("lab_y", "Y-axis:", value = "")
),
checkboxInput(inputId = "adj_fnt_sz",
label = "Change font size",
value = FALSE),
conditionalPanel(
condition = "input.adj_fnt_sz == true",
numericInput("fnt_sz_title", "Plot title:", value = 24),
numericInput("fnt_sz_labs", "Axis titles:", value = 24),
numericInput("fnt_sz_ax", "Axis labels:", value = 18),
numericInput("fnt_sz_cand", "Labels of hits:", value = 6)
),
checkboxInput(inputId = "add_legend",
label = "Add legend",
value = FALSE),
#
# conditionalPanel(
# condition = "input.add_legend == true",
# textInput("legend_title", "Legend title:", value = "")
# ),
NULL),
conditionalPanel(
condition = "input.tabs=='iPlot'", NULL),
conditionalPanel(
condition = "input.tabs=='Data'",
h4("Data upload"),
radioButtons(
"data_input", "",
choices =
list("Example data 1" = 1,
"Example data 2" = 2,
"Upload file (CSV, text, excel)" = 3,
"URL (CSV files only)" = 5
)
,
selected = 1),
conditionalPanel(
condition = "input.data_input=='1'",p('Data of differentially expressed genes in livers of mice on a high-fat-high-cholesterol diet - from figure 4C of Becares et al (2019): https://doi.org/10.1016/j.celrep.2018.12.094'),hr()),
conditionalPanel(
condition = "input.data_input=='2'",p('Data of potential interactors of Cdc42 - from Figure 9A of Gillingham et al (2019): https://doi.org/10.7554/eLife.45916.001'),hr()),
conditionalPanel(
condition = "input.data_input=='3'",
fileInput("upload", NULL, multiple = FALSE, accept = c(".xlsx", ".xls", ".txt", ".csv")),
# selectInput("file_type", "Type of file:",
# list(".csv or .txt" = "text",
# ".xls or .xlsx" = "excel"
# ),
# selected = "text"),
# radioButtons(
# "upload_delim", "Delimiter",
# choices =
# list("Comma" = ",",
# "Tab" = "\t",
# "Semicolon" = ";",
# "Space" = " ")),
# selected = ","),
selectInput("upload_delim", label = "Select Delimiter (for text file):", choices =list("Comma" = ",",
"Tab" = "\t",
"Semicolon" = ";",
"Space" = " ")),
selectInput("sheet", label = "Select sheet (for excel workbook):", choices = " ")
# actionButton("submit_datafile_button", "Submit datafile")
),
### csv via URL as input
conditionalPanel(
condition = "input.data_input=='5'",
# textInput("URL", "URL", value = "https://zenodo.org/record/2545922/files/FRET-efficiency_mTq2.csv"),
textInput("URL", "URL", value = ""),
NULL
),
h4('Select X & Y variables'),
selectInput("x_var", label = "X-axis; Effect (fold change)", choices = "-"),
selectInput("y_var", label = "Y-axis; Significance (p-value)", choices = "-"),
selectInput("g_var", label = "Select column with names", choices = "-"),
selectInput("c_var", label = "Select column with categories", choices = "-"),
checkboxInput(inputId = "cat_color",
label = "Use Color to identify Categories",
value = FALSE),
# h4("Transformation"),
# checkboxInput(inputId = "transformation",
# label = "Data transformation",
# value = FALSE),
# conditionalPanel(condition = "input.transformation==true",
# selectInput("transform_var_x", label = "Transform:", choices = "-"),
#
# radioButtons(
# "transform_x", NULL,
# choices =
# list("log2" = "log2",
# "log10" = "log10",
# "-log10" = "minus_log10"),
# selected = "log2"),
#
#
#
#
# selectInput("transform_var_y", label = "Transform:", choices = "-"),
#
# radioButtons(
# "transform_y", NULL,
# choices =
# list("log2" = "log2",
# "log10" = "log10",
# "-log10" = "minus_log10"),
# selected = "minus_log10"),
#
# NULL
#
#
# ),
# conditionalPanel(
# condition = "input.transformation==true", (downloadButton("downloadTransformedData", "Download transformed data (csv)"))),
#
# hr(),
hr(),
NULL
),
conditionalPanel(
condition = "input.tabs=='About'",
#Session counter: https://gist.github.com/trestletech/9926129
h4("About"), "There are currently",
verbatimTextOutput("count"),
"session(s) connected to this app.",
hr(),
h4("Find our other dataViz apps at:"),a("https://huygens.science.uva.nl/", href = "https://huygens.science.uva.nl/")
)
), #Close sidebarPanel
# Show a plot of the generated distribution
mainPanel(
tabsetPanel(id="tabs",
tabPanel("Data", h4("Data as provided"),dataTableOutput("uploaded")),
tabPanel("Plot",h3("Volcano Plot"
),
downloadButton("downloadPlotPDF", "Download pdf-file"),
# downloadButton("downloadPlotSVG", "Download svg-file"),
downloadButton("downloadPlotPNG", "Download png-file"),
actionButton("settings_copy", icon = icon("clone"),
label = "Clone current setting"),
div(
style = "position:relative",
plotOutput("coolplot",
height = 'auto',
# click = "clicked",
hover = hoverOpts("plot_hover", delay = 10, delayType = "debounce")),uiOutput("hover_info")
),
conditionalPanel(
condition = "input.show_table == true",
br(),h3("Top hits (based on distance from origin)"), withSpinner(dataTableOutput('toptableDT')))
),
tabPanel("iPlot", h3("Volcano Plot"),
div(downloadButton("downloadHTML", "Download html file"),
girafeOutput("iplot", height="600", width="800"), style = "float:left"),
NULL),
tabPanel("About", includeHTML("about.html"))
)
) #Close mainPanel
) #Close sidebarLayout
) #Close fluidPage
server <- function(input, output, session) {
# query_modal <- modalDialog(
# title = HTML("If this version does not run correctly, you may try these mirrors:
# <a href='https://huygens.science.uva.nl/VolcaNoseR2/'>https://huygens.science.uva.nl/VolcaNoseR2/</a></br>
# <a href='https://goedhart.shinyapps.io/VolcaNoseR/'>https://goedhart.shinyapps.io/VolcaNoseR/</a>"),
# easyClose = T,
# footer = tagList(
# 'Dismiss with <escape> key or clicking outside of the window'
# )
# )
#
query_modal <- modalDialog(
title = HTML("This version has improved support for interactive graphics on the 'iPlot' tab:
<ul>
<li>Point-and-click to (de)select hits manually</li>
<li>Lasso tool for selecting multiple hits at once</li>
<li>Option to download an interactive version of the plot as html</li>
<li>Improved hovering when using multiple screens</li>
</ul>
</br>
Any feedback on how the iPlot version compares to the original output (on the Plot tab) would be appreciated!</br>"),
easyClose = T,
footer = tagList(
'Dismiss with <escape> key or clicking outside of the window'
)
)
# Show the model on start up ...
showModal(query_modal)
# Session variable - initialize defaults
genelist.selected <- ""
x_var.selected <- "log2_FoldChange"
y_var.selected <- "minus_log10_pvalue"
g_var.selected <- "Gene"
c_var.selected <- "-"
sheet.selected <- " "
# transform_var_x.selected <- "-"
# transform_var_y.selected <- "-"
isolate(vals$count <- vals$count + 1)
###### DATA INPUT ###################
df_upload <- reactive({
if (input$data_input == 1) {
x_var.selected <<- "log2_FoldChange"
y_var.selected <<- "minus_log10_pvalue"
g_var.selected <<- "Gene"
genelist.selected <<- ""
# updateCheckboxInput(session, "transformation", value = FALSE)
# transform_var_x.selected <<- "-"
# transform_var_y.selected <<- "-"
data <- df_example_diffgenes_HFHC
} else if (input$data_input == 2) {
x_var.selected <<- "log2_FoldChange"
y_var.selected <<- "minus_log10_pvalue"
g_var.selected <<- "Gene"
genelist.selected <<- "HSPA6"
# updateCheckboxInput(session, "transformation", value = FALSE)
# transform_var_x.selected <<- "-"
# transform_var_y.selected <<- "-"
data <- df_example_cdc42
} else if (input$data_input == 3) {
genelist.selected <<- ""
# updateCheckboxInput(session, "transformation", value = FALSE)
# transform_var_x.selected <<- "-"
# transform_var_y.selected <<- "-"
file_in <- input$upload
# Avoid error message while file is not uploaded yet
if (is.null(input$upload)) {
return(data.frame(x = "Click 'Browse...' to select a datafile or drop file onto 'Browse' button"))
# } else if (input$submit_datafile_button == 0) {
# return(data.frame(x = "Press 'submit datafile' button"))
} else {
#Isolate extenstion and convert to lowercase
filename_split <- strsplit(file_in$datapath, '[.]')[[1]]
fileext <- tolower(filename_split[length(filename_split)])
# observe({print(fileext)})
# isolate({
# data <- read.csv(file=file_in$datapath, sep = input$upload_delim, na.strings=c("",".","NA", "NaN", "#N/A", "#VALUE!"))
if (fileext == "txt" || fileext=="csv") {
data <- read.csv(file=file_in$datapath, sep = input$upload_delim, na.strings=c("",".","NA", "NaN", "#N/A", "#VALUE!"))
updateSelectInput(session, "sheet", choices = " ", selected = " ")
} else if (fileext=="xls" || fileext=="xlsx") {
names <- excel_sheets(path = input$upload$datapath)
# updateSelectInput(session, "sheet_names", choices = names)
sheet.selected <<- input$sheet
updateSelectInput(session, "sheet", choices = names, selected = sheet.selected)
if (input$sheet %in% names)
{
n <- which(names==input$sheet)
# sheet.selected <<- input$sheet
} else {
n <- 1
#Ensures update and selection of first sheet upon loading the data
updateSelectInput(session, "sheet", choices = names)
}
# names <- excel_sheets(path = input$upload$datapath)
# updateSelectInput(session, "sheet_names", choices = names)
data <- readxl::read_excel(file_in$datapath, sheet = n , na = c("",".","NA", "NaN", "#N/A", "#VALUE!", "#DIV/0!"))
}
# })
}
} else if (input$data_input == 5) {
# genelist.selected <<- ""
# updateCheckboxInput(session, "transformation", value = FALSE)
# transform_var_x.selected <<- "-"
# transform_var_y.selected <<- "-"
#Read data from a URL
#This requires RCurl
if(input$URL == "") {
return(data.frame(x = "Enter a full HTML address, for example: https://zenodo.org/record/3713174/files/CSV_1-GFP-CSB-WT_vs_GFP-NLS.csv"))
} else if (url.exists(input$URL) == FALSE) {
return(data.frame(x = paste("Not a valid URL: ",input$URL)))
} else {data <- read.csv(input$URL)}
}
#Replace space and dot of header names by underscore
data <- data %>% select_all(~gsub("\\s+|\\.", "_", .))
return(data)
})
#### DISPLAY UPLOADED DATA (as provided) ##################
output$uploaded <- renderDataTable(
# observe({ print(input$tidyInput) })
df_upload(),
# df_transformed(),
rownames = FALSE,
options = list(pageLength = 20, autoWidth = FALSE,
lengthMenu = c(20, 100, 1000, 10000)),
editable = FALSE
# ,selection = 'none'
)
############## Export Normalized data in tidy format ###########
# output$downloadTransformedData <- downloadHandler(
#
# filename = function() {
# paste("VolcaNoseR_transformed", ".csv", sep = "")
# },
# content = function(file) {
# write.csv(df_transformed(), file, row.names = FALSE)
# }
# )
##### Get Variables from the input ##############
observe({
#Retrieve the currently selected geom and use as default, even when y_var changes
# if (input$transformation != TRUE) {
df <- df_upload()
# } else if (input$transformation == TRUE) {
# transform_var_x.selected <<- input$transform_var_x
# transform_var_y.selected <<- input$transform_var_y
# df <- df_transformed()
# }
var_names <- names(df)
# Get the names of columns that are factors.
nms_fact <- names(Filter(function(x) is.factor(x) || is.integer(x) || is.logical(x) || is.character(x), df))
nms_var <- names(Filter(function(x) is.integer(x) || is.numeric(x) || is.double(x), df))
nms_fact <- c("-",nms_fact)
# Pre-selection works well when example 1 or 2 is selected, but may interfere with URL-loading
# updateSelectInput(session, "x_var", choices = nms_var, selected = "log2_FoldChange")
# updateSelectInput(session, "y_var", choices = nms_var, selected = "minus_log10_pvalue")
updateSelectInput(session, "x_var", choices = nms_var, selected = x_var.selected)
updateSelectInput(session, "y_var", choices = nms_var, selected = y_var.selected)
# updateSelectInput(session, "map_size", choices = mapping_list_all)
updateSelectInput(session, "g_var", choices = nms_fact, selected = g_var.selected)
updateSelectInput(session, "c_var", choices = nms_fact, selected = c_var.selected)
updateSelectizeInput(session, "user_gene_list", selected = genelist.selected)
# updateSelectInput(session, "transform_var_x", choices = c("-",nms_var), selected = transform_var_x.selected)
# updateSelectInput(session, "transform_var_y", choices = c("-",nms_var), selected = transform_var_y.selected)
})
########### GET INPUT VARIABLEs FROM HTML ##############
observe({
query <- parseQueryString(session$clientData$url_search)
############ ?url ################
if (!is.null(query[['url']])) {
# updateRadioButtons(session, "data_input", selected = 5)
updateTextInput(session, "URL", value= query[['url']])
observe(print((query[['url']])))
# updateTabsetPanel(session, "tabs", selected = "Plot")
}
############ ?data ################
if (!is.null(query[['data']])) {
presets_data <- query[['data']]
presets_data <- unlist(strsplit(presets_data,";"))
observe(print((presets_data)))
updateRadioButtons(session, "data_input", selected = presets_data[1])
# updateCheckboxInput(session, "tidyInput", value = presets_data[2])
# updateSelectInput(session, "x_var", selected = presets_data[3])
# updateSelectInput(session, "y_var", selected = presets_data[4])
# updateSelectInput(session, "g_var", selected = presets_data[5])
x_var.selected <<- presets_data[3]
y_var.selected <<- presets_data[4]
g_var.selected <<- presets_data[5]
if (presets_data[1] == "1" || presets_data[1] == "2") {
updateTabsetPanel(session, "tabs", selected = "Plot")
}
}
############ ?vis ################
if (!is.null(query[['vis']])) {
presets_vis <- query[['vis']]
presets_vis <- unlist(strsplit(presets_vis,";"))
observe(print((presets_vis)))
fc_cutoff <- as.numeric(strsplit(presets_vis[3],",")[[1]])
if (length(fc_cutoff)<2) {
fc_cutoff[2] <- fc_cutoff[1]
min_max <- paste(fc_cutoff,collapse = ",")
} else {min_max <- fc_cutoff}
updateSliderInput(session, "pointSize", value = presets_vis[1])
updateSliderInput(session, "alphaInput", value = presets_vis[2])
updateTextInput(session, "fc_cutoff", value = min_max)
updateNumericInput(session, "p_cutoff", value = presets_vis[4])
updateSelectInput(session, "direction", selected = presets_vis[5])
updateSelectInput(session, "criterion", selected = presets_vis[6])
}
############ ?can ################
if (!is.null(query[['can']])) {
presets_can <- query[['can']]
presets_can <- unlist(strsplit(presets_can,";"))
updateNumericInput(session, "top_x", value = presets_can[1])
updateCheckboxInput(session, "show_table", value = presets_can[2])
updateCheckboxInput(session, "hide_labels", value= presets_can[3])
# updateCheckboxInput(session, "user_selected", value= presets_can[4])
# updateTextInput(session, "user_gene_list", value= presets_can[4])
genelist.selected <<- unlist(strsplit(presets_can[4],","))
# observe({print(genelist.selected)})
}
############ ?layout ################
if (!is.null(query[['layout']])) {
presets_layout <- query[['layout']]
presets_layout <- unlist(strsplit(presets_layout,";"))
# observe(print((presets_layout)))
updateCheckboxInput(session, "rotate_plot", value = presets_layout[1])
updateCheckboxInput(session, "add_grid", value = (presets_layout[2]))
updateCheckboxInput(session, "change_scale", value = presets_layout[3])
updateTextInput(session, "range_x", value= presets_layout[4])
updateTextInput(session, "range_y", value= presets_layout[5])
# updateCheckboxInput(session, "transform", value = presets_layout[6])
# updateRadioButtons(session, "transform_x", selected = presets_layout[7])
# updateRadioButtons(session, "transform_y", selected = presets_layout[8])
# updateCheckboxInput(session, "add_description", value = presets_layout[9])
if ((presets_layout[6])=='X') {
updateNumericInput(session, "plot_height", value= presets_layout[7])
updateNumericInput(session, "plot_width", value= presets_layout[8])
}
# updateTabsetPanel(session, "tabs", selected = "Plot")
}
############ ?color ################
if (!is.null(query[['color']])) {
presets_color <- query[['color']]
presets_color <- unlist(strsplit(presets_color,";"))
updateSelectInput(session, "adjustcolors", selected = presets_color[1])
updateTextInput(session, "user_color_list", value= presets_color[2])
}
############ ?label ################
if (!is.null(query[['label']])) {
presets_label <- query[['label']]
presets_label <- unlist(strsplit(presets_label,";"))
updateCheckboxInput(session, "add_title", value = presets_label[1])
updateTextInput(session, "title", value= presets_label[2])
updateCheckboxInput(session, "label_axes", value = presets_label[3])
updateTextInput(session, "lab_x", value= presets_label[4])
updateTextInput(session, "lab_y", value= presets_label[5])
updateCheckboxInput(session, "adj_fnt_sz", value = presets_label[6])
updateNumericInput(session, "fnt_sz_title", value= presets_label[7])
updateNumericInput(session, "fnt_sz_labs", value= presets_label[8])
updateNumericInput(session, "fnt_sz_ax", value= presets_label[9])
updateNumericInput(session, "fnt_sz_cand", value= presets_label[10])
updateCheckboxInput(session, "add_legend", value = presets_label[11])
# updateTextInput(session, "legend_title", value= presets_label[12])
}
############ ?url ################
if (!is.null(query[['url']])) {
updateRadioButtons(session, "data_input", selected = 5)
updateTextInput(session, "URL", value= query[['url']])
# observe(print((query[['url']])))
updateTabsetPanel(session, "tabs", selected = "Plot")
}
})
########### RENDER URL ##############
output$HTMLpreset <- renderText({
url()
})
######### GENERATE URL with the settings #########
url <- reactive({
base_URL <- paste(sep = "", session$clientData$url_protocol, "//",session$clientData$url_hostname, ":",session$clientData$url_port, session$clientData$url_pathname)
data <- c(input$data_input, "", input$x_var, input$y_var, input$g_var)
# vis <- c(input$pointSize, input$alphaInput, input$fc_cutoff, input$p_cutoff, input$direction, input$criterion)
#Convert upper/lower boundary to comma seperated values
fc <- input$fc_cutoff
fc <- paste(fc, collapse=",")
vis <- c(input$pointSize, input$alphaInput, fc, input$p_cutoff, input$direction, input$criterion)
#Convert the list of genes to a comma-seperated string
a <- input$user_gene_list
a <- paste(a, collapse=",")
# observe({print(a)})
#as.character is necessary; if omitted TRUE is converted to 0 and FALSE to 1 which is undesired
can <- c(input$top_x, as.character(input$show_table), input$hide_labels, a)
layout <- c(input$rotate_plot, input$add_grid, input$change_scale, input$range_x, input$range_y, "X", input$plot_height, input$plot_width)
#Hide the standard list of colors if it is'nt used
if (input$adjustcolors != "5") {
color <- c(input$adjustcolors, "none")
} else if (input$adjustcolors == "5") {
color <- c(input$adjustcolors, input$user_color_list)
}
############ COLOR ##########
label <- c(input$add_title, input$title, input$label_axes, input$lab_x, input$lab_y, input$adj_fnt_sz, input$fnt_sz_title, input$fnt_sz_labs, input$fnt_sz_ax, input$fnt_sz_cand, input$add_legend, input$legend_title, input$hide_labels_y)
#replace FALSE by "" and convert to string with ; as seperator
data <- sub("FALSE", "", data)
data <- paste(data, collapse=";")
data <- paste0("data=", data)
vis <- sub("FALSE", "", vis)
vis <- paste(vis, collapse=";")
vis <- paste0("vis=", vis)
can <- sub("FALSE", "", can)
can <- paste(can, collapse=";")
can <- paste0("can=", can)
#
layout <- sub("FALSE", "", layout)
layout <- paste(layout, collapse=";")
layout <- paste0("layout=", layout)
#
color <- sub("FALSE", "", color)
color <- paste(color, collapse=";")
color <- paste0("color=", color)
label <- sub("FALSE", "", label)
label <- paste(label, collapse=";")
label <- paste0("label=", label)
# stim <- sub("FALSE", "", stim)
# stim <- paste(stim, collapse=";")
# stim <- paste0("stim=", stim)
if (input$data_input == "5") {url <- paste("url=",input$URL,sep="")} else {url <- NULL}
# parameters <- paste(data, vis,layout,color,label,stim,url, sep="&")
parameters <- paste(data,vis,can,layout,color,label,url, sep="&")
preset_URL <- paste(base_URL, parameters, sep="?")
observe(print(parameters))
# observe(print(preset_URL))
return(preset_URL)
})
############# Pop-up that displays the URL to 'clone' the current settings ################
observeEvent(input$settings_copy , {
showModal(urlModal(url=url(), title = "Use the URL to launch VolcaNoseR with the current setting"))
})
# observeEvent(input$legend_copy , {
# showModal(urlModal(url=Fig_legend(), title = "Legend text"))
# })
################ Select top hits #########
df_top <- reactive({
df <- df_filtered()
if (input$direction =="increased") {
df <- df %>% filter(Change=="Increased")
} else if (input$direction =="decreased") {
df <- df %>% filter(Change=="Decreased")
} else if (input$direction =="significant") {
df <- df %>% filter(Change!="Unchanged")
}
#Get the order right
df <- df %>% select(Name, Category, Change, `Fold change (log2)`,`Significance`)
if (input$criterion == "manh") {
df <- df %>% mutate(`Manhattan distance` = abs(`Significance`)+abs(`Fold change (log2)`)) %>% arrange(desc(`Manhattan distance`))
df_out <- df %>% top_n(input$top_x,`Manhattan distance`)
} else if (input$criterion == "euclid") {
df <- df %>% mutate(`Euclidean distance` = sqrt((`Significance`)^2+(`Fold change (log2)`)^2)) %>% arrange(desc(`Euclidean distance`))
df_out <- df %>% top_n(input$top_x,`Euclidean distance`)
} else if (input$criterion == "fc") {
df <- df %>% arrange(desc(abs(`Fold change (log2)`)))
df_out <- df %>% top_n(input$top_x,abs(`Fold change (log2)`))
} else if (input$criterion == "sig") {
df <- df %>% arrange(desc(`Significance`))
df_out <- df %>% top_n(input$top_x,`Significance`)
}
#Add user selected hits, but remove them when already present
df_out <- bind_rows(df_out,df_user()) %>% distinct(Name, .keep_all = TRUE)
# }
df_out$Change <- factor(df_out$Change, levels=c("Unchanged","Increased","Decreased", "Selected"))
observe({print(df_out)})
return(df_out)
})
################ List of user-selected hits #########
df_user <- reactive({
df <- as.data.frame(df_filtered())
#select based on text input
usr_selection <- c(input$user_gene_list,input$iplot_selected)
df_selected_by_name <- df %>% filter(Name %in% usr_selection)
# clicked <- nearPoints(df, input$clicked)
# observe({print(clicked)})
#Select rows from DT
table_selection <- input$uploaded_rows_selected
# observe({print(table_selection)})
if (length(table_selection)>=1){
df_selected_by_tab <- df %>% slice(table_selection)
df_selected_by_name <- df_selected_by_name %>% bind_rows(df_selected_by_tab)
}
return(df_selected_by_name)
})
observeEvent( input$iplot_selected,{
#If selected items are new, add them
if (length(intersect(input$iplot_selected,input$user_gene_list))==0) {
genelist.selected <<- c(input$user_gene_list,input$iplot_selected)
updateSelectizeInput(session, "user_gene_list", selected = genelist.selected)
#if not, invert selection
} else {
common <- intersect(input$user_gene_list,input$iplot_selected)
combined <- union(input$user_gene_list,input$iplot_selected)
genelist.selected <<- combined[! combined %in% common]
updateSelectizeInput(session, "user_gene_list", selected = genelist.selected)
}
})
################ LOG TRANSFORM DATA #########
# df_transformed <- reactive({
#
# df <- df_upload()
#
# x_transform <- input$transform_var_x
# y_transform <- input$transform_var_y
#
#
#
# if (input$transform_x =="log2" && x_transform !="-") {
# log_name <- paste0(input$transform_x,"_",input$transform_var_x)
# df <- df %>% mutate(!!log_name := log2(df[, x_transform]))
# } else if (input$transform_x =="log10" && x_transform !="-") {
# log_name <- paste0(input$transform_x,"_",input$transform_var_x)
# df <- df %>% mutate(!!log_name := log10(df[, x_transform]))
# } else if (input$transform_x =="minus_log10" && x_transform !="-") {
# log_name <- paste0("-Log10_",input$transform_var_x)
# df <- df %>% mutate(!!log_name := -log10(df[, x_transform]))
# }
#
# if (input$transform_y =="log2" && y_transform !="-") {
# log_name <- paste0(input$transform_y,"_",input$transform_var_y)
# df <- df %>% mutate(!!log_name := log2(df[, y_transform]))
# } else if (input$transform_y =="log10" && y_transform !="-") {
# log_name <- paste0(input$transform_y,"_",input$transform_var_y)
# df <- df %>% mutate(!!log_name := log10(df[, y_transform]))
# } else if (input$transform_y =="minus_log10" && y_transform !="-") {
# log_name <- paste0("-Log10_",input$transform_var_y)
# df <- df %>% mutate(!!log_name := -log10(df[, y_transform]))
# }