Saving Dynamically Generated Plots in Shiny - r

Question

so I have recently adapted some code that I found on StackOverflow to create a dynamic number of plots based on user input. However, I now cannot figure out how to save all of those dynamic plots in one file; when I use ggsave() in downloadHandler, it only saves the last plot generated, as the plots are created inside of a for loop, inside of an observe function. I have tried saving the for loop as a separate function and saving that instead of last plot, I have tried saving the observe() as a function and calling that inside ggsave(), but nothing works. Any idea how I can save all of the generated plots to one file?
ui <- fluidPanel(
sidebarLayout(
sidebarPanel(
#this is the input widget for dataset selection
selectInput(inputId = "dataset_selec",
label = "Choose which Dataset to explore:",
choices = list("NK AD Dataset (Zhang, 2020)",
"APPPS1 Dataset (Van Hove, 2019)",
"Aging T Cell Dataset (Dulken, 2019)"),
selected = "APPPS1 Dataset (Van Hove, 2019)"))
mainPanel(
fluidRow(
column(4,
textInput(inputId = "gene_fp",
label = "Enter gene(s) of interest here, separated by commas: ")
),
column(4,
br(),
checkboxInput("split_fp", "Split the graph?")
),
column(4,
conditionalPanel(condition = "input.split_fp == true",
#display choices to split by
selectInput(inputId = "metadata_split_fp",
label = "Choose how to split the Seurat data: ",
choices = list("Genotype", "Timepoint")))
)
),
#ask users if they want to split the graphs
br(),
fluidRow(
column(4,
textInput("save_name_fp",
label = "Enter a file name: ")
),
column(4,
conditionalPanel(condition = "input.save_name_fp.length > 0",
selectInput("fp_device",
label = "Select file type: ",
choices = list("PNG", "JPEG", "PDF", "TIFF",
"BMP", "SVG")))
),
column(4,
br(),
conditionalPanel(condition = "input.save_name_fp.length > 0",
downloadButton("fp_save", label = "Save Feature Plot"))
)
),
#plot the actual plot
uiOutput("fp_plots")
)
)
)
server <- function(input, output, session) {
datasetInput <- reactive({
switch(input$dataset_selec,
"NK AD Dataset (Zhang, 2020)" = nk_data,
"APPPS1 Dataset (Van Hove, 2019)" = appps1_data,
"Aging T Cell Dataset (Dulken, 2019)" = tcellinfil_data)
})
output$fp_plots <- renderUI({
#validate is to prevent an error message from being displayed when a gene hasn't been entered yet
validate(
need(input$gene_fp !="", "Please enter a gene.")
)
fp_genes <- input$gene_fp
fp_genes <- gsub(" ", "", fp_genes)
fp_genes <- unlist(strsplit(fp_genes, split = ","))
n <- length(fp_genes)
plot_output_list <- lapply(1:n, function(i) {
plotname <- paste("plot", i, sep = "")
if (input$split_fp == TRUE) {plotOutput(plotname, height = 580, width = 1100)}
else {plotOutput(plotname, height = 580, width = 550)}
})
do.call(tagList, plot_output_list)
})
#Here, we take the input of genes, and turn it into a character vector, so that we can iterate
#over it. This needs to be under observe({}) because it involves an input.
#Next, we iterate through the list of genes using a for loop, and within that for loop we assign
#the plots that we want to be displayed to each plotname, which is also sequentially created within
#this for loop, and assign it to the tagList we generated earlier. Basically, we're adding objects to
#list of names we made earlier.
#This needs to be under local({}) control, otherwise each graph doesn't get its own number,
#because of when renderPlot is evaluated
observe({
fp_genes <- input$gene_fp
fp_genes <- gsub(" ", "", fp_genes)
fp_genes <- unlist(strsplit(fp_genes, split = ","))
for (i in 1:length(fp_genes)) {
local({
plotname <- paste("plot", i, sep = "")
gene <- fp_genes[i]
output[[plotname]] <- renderPlot({
if (input$split_fp == TRUE) {FeaturePlot(datasetInput(), features = gene, split.by = input$metadata_split_fp)}
else {FeaturePlot(datasetInput(), features = gene)}
})
})
}
})
output$fp_save <- downloadHandler(
filename = function() {
paste(input$save_name_fp, tolower(input$fp_device), sep = ".")
},
content = function(file) {
ggsave(file, device = tolower(input$fp_device))
}
)
}

Answer 1

Create a list of plots, use grid.arrange to save it in a format you wish, and then save it. Perhaps you can adapt this code.
library(shiny)
library(dplyr)
library(tidyr)
library(ggplot2)
library(gridExtra)
mean_data <- data.frame(
Name = c(paste0("Group_", LETTERS[1:20])),
matx <- matrix(sample(1:1000, 1000, replace = T), nrow = 20)
)
names(mean_data)[-1] <- c(paste0("Gene_", 1:50))
sd_data <- data.frame(
Name = c(paste0("Group_", LETTERS[1:20])),
matx <- matrix(runif(1000, 5, 10), nrow = 20)
)
names(sd_data)[-1] <- c(paste0("Gene_", 1:50))
# Prepare dataset.
# 1. Bind mean and sd data
# 2. Reshape
data <- bind_rows(list(
mean = mean_data,
sd = sd_data
), .id = "stat")
data_mean_sd1 <- data %>%
pivot_longer(-c(Name, stat), names_to = "Gene", values_to = "value") %>%
pivot_wider(names_from = "stat", values_from = "value")
###
ui <- fluidPage(
pageWithSidebar(
headerPanel("Gene_FPKM Value Barplot"),
sidebarPanel(
selectInput(
"selectGeneSymbol",
"Select Gene Symbol:",
choices = unique(data_mean_sd1$Gene),
multiple =F,
width = 400,
selected = 1 #"Igfbp7"
),
selectInput(
"selectGeneSymbol2",
"Select Gene Symbol2:",
choices = unique(data_mean_sd1$Gene),
multiple =F,
width = 400,
selected = 1 #"Igfbp7"
),
selectInput("fp_device",
label = "Select file type: ",
choices = list("PNG", "JPEG", "PDF", "TIFF","BMP", "SVG")
),
actionButton(inputId = "plot1", label = "FPKM"),
actionButton(inputId = "plot2", label = "logFC"),
actionButton(inputId = "all",label = "logFC&FPKM"),br(),
downloadButton("fp_save", label = "Save Feature Plot")
),
mainPanel(
uiOutput("all")
)
)
)
server <- function(input, output, session) {
plot_data1 <- reactive({
subset(data_mean_sd1, Gene %in% input$selectGeneSymbol)
})
plot_data2 <- reactive({
subset(data_mean_sd1, Gene %in% input$selectGeneSymbol2)
})
global <- reactiveValues(out = NULL)
observeEvent(input$plot1, {
global$out <- plotOutput("plot1", height=750)
})
observeEvent(input$plot2, {
global$out <- plotOutput("plot2", height=750)
})
observeEvent(input$all, {
global$out <- plotOutput("plot3", height=1150)
})
output$all <- renderUI({
global$out
})
p1 <- eventReactive(list(input$plot1,
input$all), {
ggplot(data = plot_data1(), aes(x = Name, y = mean,fill=Name)) +
geom_bar(stat = "identity", position = position_dodge(0.9), width = 0.9) +
geom_errorbar(aes(ymin = mean - sd, ymax = mean + sd), width = .2, position = position_dodge(0.9)) +
theme_classic2() +
rotate_x_text(angle = 45) +
theme(legend.position = "none") +
labs(title = input$selectGeneSymbol, x = NULL, y = "FPKM_value") +
theme(plot.title = element_text(hjust = 0.5)) +
theme(plot.margin = unit(c(20, 5, 1, 5), "mm"))+
theme(axis.text.x=element_text(vjust=1,size=12))
})
p2 <- eventReactive(list(input$plot2,
input$all), {
ggplot(data = plot_data2(), aes(x = Name, y = mean,fill=Name)) +
geom_bar(stat = "identity", position = position_dodge(0.9), width = 0.9) +
geom_errorbar(aes(ymin = mean - sd, ymax = mean + sd), width = .2, position = position_dodge(0.9)) +
theme_classic2() +
rotate_x_text(angle = 45) +
theme(legend.position = "none") +
labs(title = input$selectGeneSymbol2, x = NULL, y = "FPKM_value") +
theme(plot.title = element_text(hjust = 0.5)) +
theme(plot.margin = unit(c(20, 5, 1, 5), "mm"))+
theme(axis.text.x=element_text(vjust=1,size=12))
})
#plotlist <- do.call(tagList, list(p1(),p2()))
output$plot1 <- renderPlot({ p1() })
output$plot2 <- renderPlot({ p2() })
output$plot3 <- renderPlot({ grid.arrange(p1(),p2(), ncol=1) })
observe({
plots <- list(p1(),p2())
myplots <- do.call(grid.arrange, c(plots, ncol = 1))
output$fp_save <- downloadHandler(
filename = function() {
paste("myplots", tolower(input$fp_device), sep = ".")
},
content = function(file) {
ggsave(file, plot=myplots, device = tolower(input$fp_device))
}
)
})
}
# Create Shiny app ----
shinyApp(ui = ui, server = server)