I used grid.draw() function of ggnewscale package to get the plot
But it seems the way of download is not the same to ggplot2 type.
I used pdf() to save my plot result in shinyapp.
But when I click the download button the plot result is not picture type or not pdf
It confused me and I viewed several methods(here) but it doesn't work
I also get some advice Here
Here is my reproducible code and data:
options(encoding = "UTF-8")
library(stats)
library(openxlsx)
library(shiny)
library(dplyr)
library(tidyr)
library(ggplot2)
library(gridExtra)
library(ggpubr)
library(shinythemes)
library(ggpattern)
library(grid)
library(ggh4x)
library(ggnewscale)
library(psych)
library(DT)
library(shinyBS)
library(shinyjs)
###
data <- data.frame(
Name = c(paste0("Group_", LETTERS[1:20])),
matx <- matrix(sample(1:1000, 1000, replace = T), nrow = 20)
)
names(data)[-1] <- c(paste0("Gene_", 1:50))
Nameff<-structure(list(Name = c("8_TBI(1 month)", "9_control", "9_VEGF",
"10_control", "10_VEGF", "11_Brain Healty", "12_control_1", "12_control_2",
"12_AOD(Jnk1/2/3 ko)", "13_control", "13_Cpt1_ko(Cdh5 driven)",
"14_control", "14_Tsc2ko(Tbx4 driven)", "15_control", "15_Zmpste24 ko",
"16_control", "16_Adrenomedullin\r\nko(Cdh5 driven)", "17_Lung Healthy",
"18_control(14w)", "18_carboplatin(14w)"), Disease = c("TBI\r\n1month",
"VEGF\r\nsti_DG\r\nregion", "VEGF\r\nsti_DG\r\nregion", "VEGF\r\nsti_CA1\r\nregion",
"VEGF\r\nsti_CA1\r\nregion", "Healthy\r\n(Brain)", "AOD", "AOD",
"AOD", "CPT1\r\nko", "CPT1\r\nko", "Tsc2\r\nko", "Tsc2\r\nko",
"Zmpste\r\n_24 ko", "Zmpste\r\n_24 ko", "AM\r\nko", "AM\r\nko",
"Healthy\r\n(Lung)", "Chemo/Radio\r\n(Tibiae)", "Chemo/Radio\r\n(Tibiae)"
), Organ = c("Brain", "Brain", "Brain", "Brain", "Brain", "Brain",
"Lung", "Lung", "Lung", "Lung", "Lung", "Lung", "Lung", "Lung",
"Lung", "Lung", "Lung", "Lung", "Bone", "Bone"), fill = c("#f15a24",
"#FFFFFF", "#f15a24", "#FFFFFF", "#f15a24", "#FFFFFF", "#FFFFFF",
"#FFFFFF", "#00FF00", "#FFFFFF", "#00FF00", "#FFFFFF", "#00FF00",
"#FFFFFF", "#00FF00", "#FFFFFF", "#00FF00", "#FFFFFF", "#FFFFFF",
"#7570B3"), Condition = c("#CCCCFF", "#d9e021", "#d9e021", "#d9e021",
"#d9e021", "#CCCCFF", "#CCCCFF", "#CCCCFF", "#CCCCFF", "#fbb03b",
"#fbb03b", "#fbb03b", "#fbb03b", "#fbb03b", "#fbb03b", "#fbb03b",
"#fbb03b", "#fbb03b", "#d9e021", "#d9e021"), Organ_fill = c("#f15a24",
"#f15a24", "#f15a24", "#f15a24", "#f15a24", "#f15a24", "#00FF00",
"#00FF00", "#00FF00", "#00FF00", "#00FF00", "#00FF00", "#00FF00",
"#00FF00", "#00FF00", "#00FF00", "#00FF00", "#00FF00", "#7570B3",
"#7570B3"), Alpha = c(1, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1,
0, 1, 0, 1, 0, 0, 1)), row.names = 22:41, class = "data.frame")
####################################################################
ui <- fluidPage(
theme = shinytheme("superhero"),
##
useShinyjs(),
##
pageWithSidebar(
tags$h4(
Sys.time()),
sidebarPanel(
tags$h3("1111"),
selectInput(
"selectGeneSymbol",
"444d:",
choices = colnames(data[,-1]),
multiple =F,
width = 400,
selected = NULL
),
actionButton(inputId = "plot1", label = "down1",width=80),
actionButton(inputId = "plot2", label = "down2",width=80),
actionButton(inputId = "all",label = "down1&down2",width=120),
hr(),
tags$h5(tags$strong("down:")),
downloadButton("p1", "down1",width=120),
downloadButton("p2", "down2",width=120)
),
mainPanel(
tabsetPanel(
tabPanel(icon("home"),
uiOutput("all")
))
)
)
)
server <- function(input, output, session) {
##
plot_data1 <- reactive({
subset(data, colnames(data[,-1]) %in% input$selectGeneSymbol)
})
plot_data2 <- reactive({
subset(data, colnames(data[,-1]) %in% input$selectGeneSymbol)
})
##
global <- reactiveValues(out = NULL,
p1 = NULL,
p2 = NULL)
##
observeEvent(input$plot1, {
global$out <- plotOutput("plot1", height=600)
})
##
observeEvent(input$plot2, {
global$out <- plotOutput("plot2", height=600)
})
observeEvent(input$all, {
global$out <- plotOutput("plot3", height=600)
})
###############
output$all <- renderUI({
global$out
})
p1 <- eventReactive(list(input$plot1,
input$all), {
datamean_sd<-data.frame(
Nameff,
mean=tapply(data[,input$selectGeneSymbol],data$Name,mean),
sd=tapply(data[,input$selectGeneSymbol],data$Name,sd)
)
p<-ggplot(data = datamean_sd, aes(Name,mean, label = Name, fill=Organ)) +
geom_bar(position="dodge2", stat="identity",width = 0.85,color="black",alpha=datamean_sd$Alpha) +
facet_nested(.~Organ+Disease, scales = "free_x", space = "free_x",switch = "x")+
theme_classic2() +
theme(legend.position = "bottom",
legend.box = "horizontal",
plot.title = element_text(hjust = 0.5),
plot.margin = unit(c(5, 10, 20, 15), "mm"),
strip.background = element_rect(colour="black", fill="white"),
strip.text.x = element_text(size = 6, angle=0),
axis.text.x=element_text(size=8),
strip.placement = "outside"
) +
rotate_x_text(angle = 90)+
scale_fill_manual(name = "Organ",values = unique(datamean_sd$Organ_fill))
gt <- ggplotGrob(p)
grid::grid.newpage(); grid::grid.draw(gt)
})
p2 <- eventReactive(list(input$plot2,
input$all), {
datamean_sd<-data.frame(
Nameff,
mean=tapply(data[,input$selectGeneSymbol],data$Name,mean),
sd=tapply(data[,input$selectGeneSymbol],data$Name,sd)
)
p<-ggplot(data = datamean_sd, aes(Name,mean, label = Name, fill=Organ)) +
geom_bar(position="dodge2", stat="identity",width = 0.85,color="black",alpha=datamean_sd$Alpha) +
facet_nested(.~Organ+Disease, scales = "free_x", space = "free_x",switch = "x")+
theme_classic2() +
theme(legend.position = "bottom",
legend.box = "horizontal",
plot.title = element_text(hjust = 0.5),
plot.margin = unit(c(5, 10, 20, 15), "mm"),
strip.background = element_rect(colour="black", fill="white"),
strip.text.x = element_text(size = 6, angle=0),
axis.text.x=element_text(size=8),
strip.placement = "outside"
) +
rotate_x_text(angle = 90)+
scale_fill_manual(name = "Organ",values = unique(datamean_sd$Organ_fill))
gt <- ggplotGrob(p)
grid::grid.newpage(); grid::grid.draw(gt)
})
output$plot1 <- renderPlot({ p1() })
output$plot2 <- renderPlot({ p2() })
output$plot3 <- renderPlot({
## plot_list <- list(p1(),p2())
# grid.arrange(grob(p1(),p2(), ncol=1))
lollipop <- gTree(children = gList(p1(), p2()))
grid.draw(lollipop)
})
#download p1
output$p1 <- downloadHandler(
filename = function() {
paste0(input$selectGeneSymbol,"_123",".pdf")
},
content = function(file) {
pdf(file,width=20,height=10)
datamean_sd<-data.frame(
Nameff,
mean=tapply(data[,input$selectGeneSymbol],data$Name,mean),
sd=tapply(data[,input$selectGeneSymbol],data$Name,sd)
)
p<-ggplot(data = datamean_sd, aes(Name,mean, label = Name, fill=Organ)) +
geom_bar(position="dodge2", stat="identity",width = 0.85,color="black",alpha=datamean_sd$Alpha) +
facet_nested(.~Organ+Disease, scales = "free_x", space = "free_x",switch = "x")+
theme_classic2() +
theme(legend.position = "bottom",
legend.box = "horizontal",
plot.title = element_text(hjust = 0.5),
plot.margin = unit(c(5, 10, 20, 15), "mm"),
strip.background = element_rect(colour="black", fill="white"),
strip.text.x = element_text(size = 6, angle=0),
axis.text.x=element_text(size=8),
strip.placement = "outside"
) +
rotate_x_text(angle = 90)+
scale_fill_manual(name = "Organ",values = unique(datamean_sd$Organ_fill))
gt <- ggplotGrob(p)
grid::grid.newpage(); grid::grid.draw(gt)
dev.off()
}
)
#download p2
output$p2 <- downloadHandler(
filename = function() {
paste0(input$selectGeneSymbol,"_123",".pdf")
},
content = function(file) {
ggsave(file,p2(),width=20,height=10)
grid::grid.newpage(); grid::grid.draw(gt)
dev.off()
}
)
}
# Create Shiny app ----
shinyApp(ui = ui, server = server)
The biggest problem to me is I used the grid.draw() to create a plot in p1() in my shiny. And I don't know how to download it in downloadHandler() function.
I tried to use grid::grid.newpage(); grid::grid.draw(gt) in downloadHandler() but it doesn't work.
I found a stupid solution that is run the code of p1() in downloadHandler() again so I can download it but it is complex you know.
Just like this:
https://stackoverflow.com/questions/46499719/error-in-using-heatmap-as-the-plot-input-of-ggsave
I know there is something wrong in my download code. But I need your help to deal with it.
I need the right way to download grid.draw(plot) result in shinyapp.
I found a not perfectly way to download p1 or p2 in downloadHandler() but I need a better way to deal with it.
And all of p1 and p2 are grid types .I'd like to output them togather . But it doesn't work when I use grid.arrange(p1(),p2()) function. Because it is used for ggplot2 type.
#########
My first question: how to download p1 or p2 in a better way because of the grid type plot.
My second question: how to output p1() and p2() togathere just like grid.arrange() function?
Vary thanks.
