app/modules/erp_plot.R
In JesseRed/dataVis: What the Package Does (One Line, Title Case)
library(shiny)
library(markdown)
library(corrr)
library(GGally)
library(ggcorrplot)
library(ggplot2)
library(plotly)
ERPPlotUI <- function(id){
ns <- NS(id)
tagList(
uiOutput(ns("fluidRow_oben")),
# absolutePanel(
# bottom = 20, right = 20, width = 200,
# draggable = TRUE,
# wellPanel(
# htmlOutput(ns("html_text")),
# sliderInput("n", "", min=3, max=20, value=5),
# plotOutput("plot2", height="200px")
#
# ),
# style = "opacity: 0.92"
# ),
)
}
ERPPlotServer <- function(id) {
moduleServer(
id,
function(input, output, session) {
ns<-session$ns
output$fluidRow_oben <- renderUI({
fluidPage(
fluidRow(
column(12,
h4("ERP Plots", align = "center")
)
)
)
}
)
}
)
}
# fluidRow(
# column(4,
#
# style = "background-color: #fcfcfc;",
# #style = 'border-bottom: 2px solid gray',
# style = "border-right: 2px solid black",
# h4("group comparison", align = "center"),
# fluidRow(
# column(6,
# selectInput(ns("group1"), h5("Select Group1", align = "center"),
# choices = g_groups(), selected = g_groups()[2])
# ),
# column(6,
# selectInput(ns("group2"), h5("Select Group 2", align = "center"),
# choices = g_groups(), selected = g_groups()[3])
# )
# )
# ),
# column(4,
# style = "background-color: #fcfcfc;",
# style = 'border-right: 2px solid gray',
# h4("trial comparison", align = "center"),
# fluidRow(
# column(6,
# selectInput(ns("trial1"), h5("Select Trial 1", align = "center"),
# choices = g_trials_named(), selected = g_groups()[1])
# ),
# column(6,
# selectInput(ns("trial2"), h5("Select Trial 2", align = "center"),
# choices = g_trials_named(), selected = g_groups()[2])
# )
# )
# ),
# column(2,
# style = "background-color: #fcfcfc;",
# h4("Visualize", align = "center"),
# selectInput(ns("method"), h5("method"),
# choices = c("Corrplot", "Corrplot_mixed", "Corrplot_clustered", "ggcorr", "Circle", "Pheatmap"), selected = 1)
# ),
# column(2,
# fluidRow(
# column(6,
# numericInput(ns("plot_height"),"plot height",800)
# ),
# column(6,
# numericInput(ns("plot_width"),"plot width",0)
# ),
# ),
# fluidRow(
# column(6,
# numericInput(ns("plot_res"),"res",96),
# ),
# column(6,
# actionButton(ns("ExportData"), "export Data"),
# ),
# ),
# )
# ),
# fluidRow(
# plotOutput(ns("plot"), width = "auto", height = "800px", click = ns("plot_click"))
# ),
#
# fluidRow(
# column(9,
# plotOutput(ns("hist"), width = "auto", height = "300px", click = ns("plot_click_hist")),
# ),
# column(3,
# verbatimTextOutput(ns("text_bottom")),
# fluidRow(
# column(6,
# numericInput(ns("nif_click_x"),"x=",1),
# ),
# column(6,
# numericInput(ns("nif_click_y"),"y=",2),
# ),
# ),
# fluidRow(
# column(6,
# textInput(ns("nif_click_x_region"),"x=","no selection"),
# ),
# column(6,
# textInput(ns("nif_click_y_region"),"y=","no selection"),
# ),
# ),
# )
# ),
# # fluidRow(
# # column(2, actionButton(ns("saveImage"), "save Image"),),
# # column(2, textInput(ns("saveimage_filename"),"filename ","mycompplotimage")),
# # column(2, numericInput(ns("saveimage_height"),"height (cm)",8)),
# # column(2, numericInput(ns("saveimage_width"),"width (cm)",8)),
# # column(2, numericInput(ns("saveimage_dpi"),"dpi",600)),
# # column(2, selectInput(ns("saveimage_fileformat"), "file format", choices = c("tiff", "pdf", "png"))),
# # ),
# fluidRow(
# column(12,
# box(title = "Plot ..........expand for help (comp_plot_markdown.md)", width = 12, collapsible = TRUE, collapsed = TRUE, htmlOutput(ns("htmlhelp_Comp_Plot"))),
# )
# ),
# fluidRow(
# plotlyOutput(ns("myplotly"), width = "1000", height = "800px")
# ),
#
# )
# })
#
# x1<<- NULL
# x2<<- NULL
# myTabPlots <<- list()
#
# # filter data by group
# data_freqmean <- reactive({
# get_data_freqmean(g_data(), g_sel_freqs())
# })
# #
# # click_x_num <- reactive({ round(input$plot_click$x)})
# # click_y_num <- reactive({ abs(round(input$plot_click$y)-length(g_regions())-1)})
# # click_x_reg <- reactive({ regions()[click_x_num]})
# # click_y_reg <- reactive({ regions()[click_y_num]})
#
# ####################################################################################
# ####################################################################################
# # The following section handels the selection of the x and y coordinate in the plot
# # a reactiveVal is needed because i need a common variable that can be changed
# # bei either the click or the change in the input field
# level_x_rval <- reactiveVal(1)
# level_y_rval <- reactiveVal(2)
# region_x_rval <- reactiveVal("not_selected")
# region_y_rval <- reactiveVal("not_selected")
# # update the textInput and numericInput depending on the reactiveVals
# observe({
# updateTextInput(session, "nif_click_x_region", value = region_x_rval())
# updateTextInput(session, "nif_click_y_region", value = region_y_rval())
# })
# # wenn die x, y Koordinate manuell verstellt wird
# observeEvent(c(input$nif_click_x, input$nif_click_y),{
# #cat(file = stderr(), "plot_text observeEvent")
# level_x_rval(input$nif_click_x)
# level_y_rval(input$nif_click_y)
# region_x_rval(g_regions()[input$nif_click_x])
# region_y_rval(g_regions()[input$nif_click_y])
# })
# # wenn in den plot geklickt wird (funktioniert nur fuer den Corplot)
# observeEvent(input$plot_click,{
# cat(file = stderr(), "plot_click observeEvent")
# level_x = round(input$plot_click$x)
# level_y = abs(round(input$plot_click$y)-length(g_regions())-1)
# region_x = (g_regions()[level_x])
# region_y = (g_regions()[level_y])
# level_x_rval(level_x)
# level_y_rval(level_y)
# region_x_rval(region_x)
# region_y_rval(region_y)
# updateNumericInput(session, "nif_click_x", value = level_x)
# updateNumericInput(session, "nif_click_y", value = level_y)
#
# })
# ####################################################################################
# ####################################################################################
#
#
# data_1 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group1, as.numeric(input$trial1), g_sel_freqs())
# })
# data_2 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group2, as.numeric(input$trial2), g_sel_freqs())
# })
# data_g1t1 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group1, as.numeric(input$trial1), g_sel_freqs())
# })
# data_g1t2 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group1, as.numeric(input$trial2), g_sel_freqs())
# })
# data_g2t1 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group2, as.numeric(input$trial1), g_sel_freqs())
# })
# data_g2t2 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group2, as.numeric(input$trial2), g_sel_freqs())
# })
#
# curdata <- reactive({
# get_currently_selected_data(g_data(), input$group1, input$group2, as.numeric(input$trial1), as.numeric(input$trial2), g_sel_freqs())
# })
#
# plotwidth <- reactive({
# if (input$plot_width == 0){ return("auto") }
# else{ return(input$plot_width) }
# })
#
# plotheight <- reactive({
# if (input$plot_height == 0){ return("auto")}
# else{ return(input$plot_height) }
# })
#
#
#
#
#
# ###########################################################
# ### RENDERPLOT
# output$myplotly<-renderPlotly({
# d <- curdata()
# mat_t <<- d$mat_t
# mat_p <<- d$mat_p
# p <-generate_plot_ggplot_corrplot_handmade(mat_p, mat_t)
# #
# # d<-tapply(PlantGrowth$weight,PlantGrowth$group,mean)
# # d<-data.frame(d)
# # d <- curdata()
# # mat_t <<- d$mat_t
# # mat_p <<- d$mat_p
# # # p<-plot_ly(x = rownames(d), y = c(input$ctrl,input$trt1,input$trt2),
# # # type ="bar"
# # # )
# #
# # # p<-layout(p,title = "Mean plantgrowth",
# # # xaxis = list(
# # # title = "GROUP",
# # # titlefont = list(size=16)
# # # ),
# # # yaxis = list(
# # # title = "MEAN GROWTH",
# # # titlefont = list(size=16),
# # # ticks="outside",
# # # ticklen=7,
# # # zeroline=TRUE,
# # # showline=TRUE
# # # )
# # # )
# #
# # #data(mtcars)
# # #corr <- round(cor(mtcars), 1)
# # #p.mat <- cor_pmat(mtcars)
# #
# # # ggcorrplot(mat_p)
# #
# # # nbreaks=8,
# # # use = "everything",
# # # palette='RdGy',
# # # label=TRUE,
# # # label_size=5,
# # # label_color='white')
# # #p<-ggcorr(data = NULL, cor_matrix=mat_p)
# # #p<-ggcorrplot(data = NULL, cor_matrix=mat_p)
# # #p<-ggcorrplot(corr)
# # #p<-ggcorr(corr, nbreaks = 5)
# # mat_p_sig = mat_p
# # mat_p_sig[mat_p_sig>0.05]=0.05000001
# # p<-ggcorr(
# # data = NULL,
# # cor_matrix = mat_p_sig,
# # nbreaks = 5,
# # label = TRUE,
# # drop = TRUE,
# # limits = FALSE #c(0,0.05)
# # )
#
# # ggcorr(nba[, 2:15], geom = "blank", label = TRUE, hjust = 0.75) +
# # geom_point(size = 10, aes(color = coefficient > 0, alpha = abs(coefficient) > 0.5)) +
# # scale_alpha_manual(values = c("TRUE" = 0.25, "FALSE" = 0)) +
# # guides(color = FALSE, alpha = FALSE)
#
#
# p
# })
# #width = function() plotwidth(),
# #height = function() plotheight(),
#
#
# ###########################################################
# ### RENDERPLOT
# output$plot<-renderPlot(
# width = function() plotwidth(),
# height = function() plotheight(),
# res = input$plot_res,
# {
# req(input$trial1)
# req(input$trial2)
# req(input$group1)
# req(input$group2)
# req(input$method)
# # dev.off()
# cur_dev <- dev.cur()
# cat(file = stderr(), cur_dev)
# d <- curdata()
# mat_t <<- d$mat_t
# mat_p <<- d$mat_p
# ###################
# # CORRPLOT
# if (input$method=="Corrplot"){
# generate_plot_Corrplot(d$mat_p, d$mat_t)
#
# }
#
#
# if (input$method=="Corrplot_mixed"){
# #png("mypng.png")
# #x1 <<- plot(d$mat_t)
# mat_p_sig <- mat_p
# mat_p_sig[mat_p>g_sig()]<-g_sig()+0.0000000001
#
# #dev.off()
# rownames(mat_p) = vector(mode="character", length=length(g_regions()))
# x1 <<- corrplot(mat_p_sig, method="circle", tl.cex = 0.9, type = "upper", is.corr = FALSE,
# p.mat = mat_p_sig, sig.level = g_sig(),
# diag=FALSE,
# insig = "blank",
# tl.srt = 45,
# col=colorRampPalette(c("blue","red","green"))(200)
# #cl.lim = c(0,g_sig())
# )
# #non_corr.method = "pch",
# #col=colorRampPalette(c("blue","red","green"))(200))
# colnames(mat_t) = vector(mode="character", length=length(g_regions()))
#
# # myplot_corr <<- corrplot(mat_t, add = TRUE, method="number", tl.cex = 0.9, type = "lower", is.corr = FALSE,
# # p.mat = mat_p, sig.level = g_sig())
#
#
# }
# if (input$method=="Corrplot_clustered"){
# #png("mypng.png")
# #x1 <<- plot(d$mat_t)
# #https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html order = "AOE"
# rownames(mat_p) = vector(mode="character", length=length(g_regions()))
# x1 <<- corrplot(mat_p, method="circle", tl.cex = 0.9, type = "upper", is.corr = FALSE,
# p.mat = mat_p, sig.level = g_sig(),
# col=colorRampPalette(c("blue","red","green"))(200))
# colnames(mat_t) = vector(mode="character", length=length(g_regions()))
#
# myplot_corr <<- corrplot(mat_t, add = TRUE, method="number", tl.cex = 0.9, type = "lower", is.corr = FALSE,
# p.mat = mat_p, sig.level = g_sig())
#
# #,
# # col=colorRampPalette(c("blue","red","green"))(200))
# #dev.off()
#
#
# }
# if (input$method=="ggcorr"){
# #png("mypng.png")
# #x1 <<- plot(d$mat_t)
# #https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html order = "AOE"
# #df <- as.data.frame(mat_p)
# #ggplot(data = df) + geom_point()
# #df <- as.data.frame(mat_p)
# #x <-ggplot(data = df, aes(x=frontopolar_A, y = central_A)) + geom_point()
# #x
# p <-generate_plot_ggplot_corrplot_handmade(mat_p, mat_t)
#
# # data(mtcars)
# # corr <- round(cor(mtcars), 1)
# # p.mat <- cor_pmat(mtcars)
# # ggcorrplot(corr)
#
# #x1 <- plot(d$mat_t)
# #ggcorr(data = NULL, cor_matrix=mat_p)
#
#
# #
# # ggcorrplot(corr, hc.order = TRUE,
# # type = "lower",
# # lab = TRUE,
# # lab_size = 3, insig = 'blank',
# # method="square", p.mat = corr, sig.level = 0.4,
# # colors = c("tomato2", "white", "springgreen3"),
# # title="Correlogram of mtcars",
# # ggtheme=theme_bw) + geom_point(aes(colour = cut(pvalue, c(-Inf, 0.1, 0.2, Inf))),
# # + size = 5) +
# # scale_color_manual(name = "pvalue",
# # values = c("(-Inf,0.1]" = "black",
# # + "(0.1,0.2]" = "yellow",
# # + "(0.2, Inf]" = "red"),
# # labels = c("<= 0.1", "0.1 < pval <= 0.2", "> 0.2"))
# #
#
#
#
#
#
#
#
#
#
#
# #
# # > corr <- matrix(runif(100),nrow=10)
# # > ggcorrplot(corr, hc.order = TRUE,
# # type = "lower",
# # lab = TRUE,
# # lab_size = 3,
# # method="circle",
# # colors = c("tomato2", "white", "springgreen3"),
# # title="Correlogram of mtcars",
# # ggtheme=theme_bw)
# # # myplot_corr
# # # cat(file = stderr(), 'ggcorr\n')
# # # ggcorrplot(mat_p)
# #
# # # nbreaks=8,
# # # use = "everything",
# # # palette='RdGy',
# # # label=TRUE,
# # # label_size=5,
# # # label_color='white')
# # mat_p_sig = mat_p
# # mat_p_sig[mat_p_sig>0.05]=0.05000001
# # # xx<-ggcorr(
# # # data = NULL,
# # # cor_matrix = mat_p_sig,
# # # nbreaks = 5,
# # # label = TRUE,
# # # drop = TRUE,
# # # limits = FALSE #c(0,0.05)
# # # )
# # df <- as.data.frame(mat_p)
# #
# # xx <- ggcorr(
# # data = NULL,
# # cor_matrix = mat_p,
# # geom = "blank",
# # digits = 3,
# # label = TRUE,
# # hjust = 0.75,
# # angle = -45) +
# #
# # geom_point(
# # size = 12,
# # aes(color = coefficient > 0,
# # alpha = abs(coefficient) < 0.05)) +
# # scale_alpha_manual(values = c("TRUE" = 0.25, "FALSE" = 0)) +
# # geom_mark(data = df)+ #, aes(p.value=mat_p))+
# # #geom_abline(slope = -1, intercept = dim(mat_p)-1)+
# # geom_abline(slope = 1, intercept = 0)+
# # guides(color = FALSE, alpha = FALSE)
# #
#
# #xx<- generate_histogram_plot_facet(input$group1, input$group2, input$trial1, input$trial2, freq(), level_x_rval(), level_y_rval())
# return(p)
# }
# if (input$method=="Circle"){
# myplotcircle = generate_plot_Circle(d$mat_p, d$mat_t, d$data1, d$data2)
#
#
# }
# if (input$method=="Pheatmap"){
#
# cur_dev <- dev.cur()
# # Pheatmat setzt das dev.cur() um ... daher manuelles zuruck setzen
# myplotpheatmap = generate_plot_Pheatmap(d$mat_p, d$mat_t, myfontsize = 18)
# #cur_dev <- dev.cur()
# #cat(file = stderr(), paste0("cur_dev=", cur_dev,"\n"))
# dev.set(cur_dev)
# return(myplotpheatmap)
#
# }
#
# }
# )
#
# output$text_bottom <- renderPrint({
# x = curdata()$data1[, level_y_rval(), level_x_rval()]
# y = curdata()$data2[, level_y_rval(), level_x_rval()]
# z = t.test(x,y, paired = curdata()$my_paired)
# out <- create_my_ttest_string(z, paired = curdata()$my_paired, mean1 = mean(x), mean2 = mean(y))
# cat(out)
# })
#
# output$hist <- renderPlot({
#
# generate_histogram_plot_facet(input$group1, input$group2, input$trial1, input$trial2, g_sel_freqs(), level_x_rval(), level_y_rval())
#
# })
#
#
# output$facet <- renderPlot({
# df = tbl_beh
# d = data_freqmean()
# df$data1 = d[,level_x_rval, level_y_rval, input$trial1]
# df$num <- ave(df$data1, df$Gruppe, FUN = seq_along)
#
# })
#
# output$htmlhelp_Comp_Plot <- renderUI({
# # if (showhtml()){
# includeMarkdown(rmarkdown::render("./documentation/comp_plot_markdown.md"))
# # }
# })
#
#
#
#
#
# # Observe Funktion fuer den zentralen Specherbutton
# observeEvent(g_saveImage_button(),{
# req(input$group1)
# req(input$group1)
# req(input$trial1)
# req(input$trial2)
#
# cat(file = stderr(), "observeEvent(g_save_Image_button(), with input$method =", input$method,"\n")
# cat(file = stderr(), "dpi=",g_saveImage_dpi(),"\n")
# d <- curdata()
# #if (g_saveImage_button()>0){
# filename = paste0(g_saveImage_filename(),"_hist", format(Sys.time(), "%Y-%m-%d-%H-%M-%S."), g_saveImage_fileext())
# myplot<-generate_histogram_plot_facet(input$group1, input$group2, input$trial1, input$trial2, g_sel_freqs(), level_x_rval(), level_y_rval())
# ggsave(file = filename, width = g_saveImage_width(), height =g_saveImage_height(), units = "cm", plot = myplot, type = "cairo", dpi = g_saveImage_dpi())
# #}
#
#
# filename2 = paste0(g_saveImage_filename(),"_",input$method, format(Sys.time(), "%Y-%m-%d-%H-%M-%S."), g_saveImage_fileext())
# open_device_for_save(filename2)
# myplot = switch(
# input$method,
# "Corrplot" = generate_plot_Corrplot(d$mat_p, d$mat_t),
# "Circle" = generate_plot_Circle(d$mat_p, d$mat_t, d$data1, d$data2),
# "Pheatmap" = generate_plot_Pheatmap(d$mat_p, d$mat_t)
# )
# dev.off()
# }
# )
#
# observeEvent(input$ExportData, {
# session$sendCustomMessage(type = 'testmessage',
# message = 'saving data now')
# #ggsave(file = "tmpbutton.png")
# #ggsave(plot = x1, filename = "x1plot.png", type = "cairo", dpi = 600)
# req(input$trial1)
# req(input$trial2)
# req(input$group1)
# req(input$group2)
# d <- curdata()
# data1 <- d$data1
# data2 <- d$data2
# string1 <-d$string1
# mat_p <- d$mat_p
# mat_t <- d$mat_t
# saveRDS(mat_p, file = "./exported_variables_from_visualizer/ExportData2D_mat_p.Rds")
# saveRDS(mat_t, file = "./exported_variables_from_visualizer/ExportData2D_mat_t.Rds")
# saveRDS(data1, file = "./exported_variables_from_visualizer/ExportData3D_data1_subj_reg1_reg2.Rds")
# saveRDS(data2, file = "./exported_variables_from_visualizer/ExportData3D_data2_subj_reg1_reg2.Rds")
#
# })
#
# }
# )
# }
JesseRed/dataVis documentation built on July 16, 2025, 8:17 p.m.
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library(shiny)
library(markdown)
library(corrr)
library(GGally)
library(ggcorrplot)
library(ggplot2)
library(plotly)
ERPPlotUI <- function(id){
ns <- NS(id)
tagList(
uiOutput(ns("fluidRow_oben")),
# absolutePanel(
# bottom = 20, right = 20, width = 200,
# draggable = TRUE,
# wellPanel(
# htmlOutput(ns("html_text")),
# sliderInput("n", "", min=3, max=20, value=5),
# plotOutput("plot2", height="200px")
#
# ),
# style = "opacity: 0.92"
# ),
)
}
ERPPlotServer <- function(id) {
moduleServer(
id,
function(input, output, session) {
ns<-session$ns
output$fluidRow_oben <- renderUI({
fluidPage(
fluidRow(
column(12,
h4("ERP Plots", align = "center")
)
)
)
}
)
}
)
}
# fluidRow(
# column(4,
#
# style = "background-color: #fcfcfc;",
# #style = 'border-bottom: 2px solid gray',
# style = "border-right: 2px solid black",
# h4("group comparison", align = "center"),
# fluidRow(
# column(6,
# selectInput(ns("group1"), h5("Select Group1", align = "center"),
# choices = g_groups(), selected = g_groups()[2])
# ),
# column(6,
# selectInput(ns("group2"), h5("Select Group 2", align = "center"),
# choices = g_groups(), selected = g_groups()[3])
# )
# )
# ),
# column(4,
# style = "background-color: #fcfcfc;",
# style = 'border-right: 2px solid gray',
# h4("trial comparison", align = "center"),
# fluidRow(
# column(6,
# selectInput(ns("trial1"), h5("Select Trial 1", align = "center"),
# choices = g_trials_named(), selected = g_groups()[1])
# ),
# column(6,
# selectInput(ns("trial2"), h5("Select Trial 2", align = "center"),
# choices = g_trials_named(), selected = g_groups()[2])
# )
# )
# ),
# column(2,
# style = "background-color: #fcfcfc;",
# h4("Visualize", align = "center"),
# selectInput(ns("method"), h5("method"),
# choices = c("Corrplot", "Corrplot_mixed", "Corrplot_clustered", "ggcorr", "Circle", "Pheatmap"), selected = 1)
# ),
# column(2,
# fluidRow(
# column(6,
# numericInput(ns("plot_height"),"plot height",800)
# ),
# column(6,
# numericInput(ns("plot_width"),"plot width",0)
# ),
# ),
# fluidRow(
# column(6,
# numericInput(ns("plot_res"),"res",96),
# ),
# column(6,
# actionButton(ns("ExportData"), "export Data"),
# ),
# ),
# )
# ),
# fluidRow(
# plotOutput(ns("plot"), width = "auto", height = "800px", click = ns("plot_click"))
# ),
#
# fluidRow(
# column(9,
# plotOutput(ns("hist"), width = "auto", height = "300px", click = ns("plot_click_hist")),
# ),
# column(3,
# verbatimTextOutput(ns("text_bottom")),
# fluidRow(
# column(6,
# numericInput(ns("nif_click_x"),"x=",1),
# ),
# column(6,
# numericInput(ns("nif_click_y"),"y=",2),
# ),
# ),
# fluidRow(
# column(6,
# textInput(ns("nif_click_x_region"),"x=","no selection"),
# ),
# column(6,
# textInput(ns("nif_click_y_region"),"y=","no selection"),
# ),
# ),
# )
# ),
# # fluidRow(
# # column(2, actionButton(ns("saveImage"), "save Image"),),
# # column(2, textInput(ns("saveimage_filename"),"filename ","mycompplotimage")),
# # column(2, numericInput(ns("saveimage_height"),"height (cm)",8)),
# # column(2, numericInput(ns("saveimage_width"),"width (cm)",8)),
# # column(2, numericInput(ns("saveimage_dpi"),"dpi",600)),
# # column(2, selectInput(ns("saveimage_fileformat"), "file format", choices = c("tiff", "pdf", "png"))),
# # ),
# fluidRow(
# column(12,
# box(title = "Plot ..........expand for help (comp_plot_markdown.md)", width = 12, collapsible = TRUE, collapsed = TRUE, htmlOutput(ns("htmlhelp_Comp_Plot"))),
# )
# ),
# fluidRow(
# plotlyOutput(ns("myplotly"), width = "1000", height = "800px")
# ),
#
# )
# })
#
# x1<<- NULL
# x2<<- NULL
# myTabPlots <<- list()
#
# # filter data by group
# data_freqmean <- reactive({
# get_data_freqmean(g_data(), g_sel_freqs())
# })
# #
# # click_x_num <- reactive({ round(input$plot_click$x)})
# # click_y_num <- reactive({ abs(round(input$plot_click$y)-length(g_regions())-1)})
# # click_x_reg <- reactive({ regions()[click_x_num]})
# # click_y_reg <- reactive({ regions()[click_y_num]})
#
# ####################################################################################
# ####################################################################################
# # The following section handels the selection of the x and y coordinate in the plot
# # a reactiveVal is needed because i need a common variable that can be changed
# # bei either the click or the change in the input field
# level_x_rval <- reactiveVal(1)
# level_y_rval <- reactiveVal(2)
# region_x_rval <- reactiveVal("not_selected")
# region_y_rval <- reactiveVal("not_selected")
# # update the textInput and numericInput depending on the reactiveVals
# observe({
# updateTextInput(session, "nif_click_x_region", value = region_x_rval())
# updateTextInput(session, "nif_click_y_region", value = region_y_rval())
# })
# # wenn die x, y Koordinate manuell verstellt wird
# observeEvent(c(input$nif_click_x, input$nif_click_y),{
# #cat(file = stderr(), "plot_text observeEvent")
# level_x_rval(input$nif_click_x)
# level_y_rval(input$nif_click_y)
# region_x_rval(g_regions()[input$nif_click_x])
# region_y_rval(g_regions()[input$nif_click_y])
# })
# # wenn in den plot geklickt wird (funktioniert nur fuer den Corplot)
# observeEvent(input$plot_click,{
# cat(file = stderr(), "plot_click observeEvent")
# level_x = round(input$plot_click$x)
# level_y = abs(round(input$plot_click$y)-length(g_regions())-1)
# region_x = (g_regions()[level_x])
# region_y = (g_regions()[level_y])
# level_x_rval(level_x)
# level_y_rval(level_y)
# region_x_rval(region_x)
# region_y_rval(region_y)
# updateNumericInput(session, "nif_click_x", value = level_x)
# updateNumericInput(session, "nif_click_y", value = level_y)
#
# })
# ####################################################################################
# ####################################################################################
#
#
# data_1 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group1, as.numeric(input$trial1), g_sel_freqs())
# })
# data_2 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group2, as.numeric(input$trial2), g_sel_freqs())
# })
# data_g1t1 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group1, as.numeric(input$trial1), g_sel_freqs())
# })
# data_g1t2 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group1, as.numeric(input$trial2), g_sel_freqs())
# })
# data_g2t1 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group2, as.numeric(input$trial1), g_sel_freqs())
# })
# data_g2t2 <- reactive({
# get_data_group_trial_freqmean(g_data(),input$group2, as.numeric(input$trial2), g_sel_freqs())
# })
#
# curdata <- reactive({
# get_currently_selected_data(g_data(), input$group1, input$group2, as.numeric(input$trial1), as.numeric(input$trial2), g_sel_freqs())
# })
#
# plotwidth <- reactive({
# if (input$plot_width == 0){ return("auto") }
# else{ return(input$plot_width) }
# })
#
# plotheight <- reactive({
# if (input$plot_height == 0){ return("auto")}
# else{ return(input$plot_height) }
# })
#
#
#
#
#
# ###########################################################
# ### RENDERPLOT
# output$myplotly<-renderPlotly({
# d <- curdata()
# mat_t <<- d$mat_t
# mat_p <<- d$mat_p
# p <-generate_plot_ggplot_corrplot_handmade(mat_p, mat_t)
# #
# # d<-tapply(PlantGrowth$weight,PlantGrowth$group,mean)
# # d<-data.frame(d)
# # d <- curdata()
# # mat_t <<- d$mat_t
# # mat_p <<- d$mat_p
# # # p<-plot_ly(x = rownames(d), y = c(input$ctrl,input$trt1,input$trt2),
# # # type ="bar"
# # # )
# #
# # # p<-layout(p,title = "Mean plantgrowth",
# # # xaxis = list(
# # # title = "GROUP",
# # # titlefont = list(size=16)
# # # ),
# # # yaxis = list(
# # # title = "MEAN GROWTH",
# # # titlefont = list(size=16),
# # # ticks="outside",
# # # ticklen=7,
# # # zeroline=TRUE,
# # # showline=TRUE
# # # )
# # # )
# #
# # #data(mtcars)
# # #corr <- round(cor(mtcars), 1)
# # #p.mat <- cor_pmat(mtcars)
# #
# # # ggcorrplot(mat_p)
# #
# # # nbreaks=8,
# # # use = "everything",
# # # palette='RdGy',
# # # label=TRUE,
# # # label_size=5,
# # # label_color='white')
# # #p<-ggcorr(data = NULL, cor_matrix=mat_p)
# # #p<-ggcorrplot(data = NULL, cor_matrix=mat_p)
# # #p<-ggcorrplot(corr)
# # #p<-ggcorr(corr, nbreaks = 5)
# # mat_p_sig = mat_p
# # mat_p_sig[mat_p_sig>0.05]=0.05000001
# # p<-ggcorr(
# # data = NULL,
# # cor_matrix = mat_p_sig,
# # nbreaks = 5,
# # label = TRUE,
# # drop = TRUE,
# # limits = FALSE #c(0,0.05)
# # )
#
# # ggcorr(nba[, 2:15], geom = "blank", label = TRUE, hjust = 0.75) +
# # geom_point(size = 10, aes(color = coefficient > 0, alpha = abs(coefficient) > 0.5)) +
# # scale_alpha_manual(values = c("TRUE" = 0.25, "FALSE" = 0)) +
# # guides(color = FALSE, alpha = FALSE)
#
#
# p
# })
# #width = function() plotwidth(),
# #height = function() plotheight(),
#
#
# ###########################################################
# ### RENDERPLOT
# output$plot<-renderPlot(
# width = function() plotwidth(),
# height = function() plotheight(),
# res = input$plot_res,
# {
# req(input$trial1)
# req(input$trial2)
# req(input$group1)
# req(input$group2)
# req(input$method)
# # dev.off()
# cur_dev <- dev.cur()
# cat(file = stderr(), cur_dev)
# d <- curdata()
# mat_t <<- d$mat_t
# mat_p <<- d$mat_p
# ###################
# # CORRPLOT
# if (input$method=="Corrplot"){
# generate_plot_Corrplot(d$mat_p, d$mat_t)
#
# }
#
#
# if (input$method=="Corrplot_mixed"){
# #png("mypng.png")
# #x1 <<- plot(d$mat_t)
# mat_p_sig <- mat_p
# mat_p_sig[mat_p>g_sig()]<-g_sig()+0.0000000001
#
# #dev.off()
# rownames(mat_p) = vector(mode="character", length=length(g_regions()))
# x1 <<- corrplot(mat_p_sig, method="circle", tl.cex = 0.9, type = "upper", is.corr = FALSE,
# p.mat = mat_p_sig, sig.level = g_sig(),
# diag=FALSE,
# insig = "blank",
# tl.srt = 45,
# col=colorRampPalette(c("blue","red","green"))(200)
# #cl.lim = c(0,g_sig())
# )
# #non_corr.method = "pch",
# #col=colorRampPalette(c("blue","red","green"))(200))
# colnames(mat_t) = vector(mode="character", length=length(g_regions()))
#
# # myplot_corr <<- corrplot(mat_t, add = TRUE, method="number", tl.cex = 0.9, type = "lower", is.corr = FALSE,
# # p.mat = mat_p, sig.level = g_sig())
#
#
# }
# if (input$method=="Corrplot_clustered"){
# #png("mypng.png")
# #x1 <<- plot(d$mat_t)
# #https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html order = "AOE"
# rownames(mat_p) = vector(mode="character", length=length(g_regions()))
# x1 <<- corrplot(mat_p, method="circle", tl.cex = 0.9, type = "upper", is.corr = FALSE,
# p.mat = mat_p, sig.level = g_sig(),
# col=colorRampPalette(c("blue","red","green"))(200))
# colnames(mat_t) = vector(mode="character", length=length(g_regions()))
#
# myplot_corr <<- corrplot(mat_t, add = TRUE, method="number", tl.cex = 0.9, type = "lower", is.corr = FALSE,
# p.mat = mat_p, sig.level = g_sig())
#
# #,
# # col=colorRampPalette(c("blue","red","green"))(200))
# #dev.off()
#
#
# }
# if (input$method=="ggcorr"){
# #png("mypng.png")
# #x1 <<- plot(d$mat_t)
# #https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html order = "AOE"
# #df <- as.data.frame(mat_p)
# #ggplot(data = df) + geom_point()
# #df <- as.data.frame(mat_p)
# #x <-ggplot(data = df, aes(x=frontopolar_A, y = central_A)) + geom_point()
# #x
# p <-generate_plot_ggplot_corrplot_handmade(mat_p, mat_t)
#
# # data(mtcars)
# # corr <- round(cor(mtcars), 1)
# # p.mat <- cor_pmat(mtcars)
# # ggcorrplot(corr)
#
# #x1 <- plot(d$mat_t)
# #ggcorr(data = NULL, cor_matrix=mat_p)
#
#
# #
# # ggcorrplot(corr, hc.order = TRUE,
# # type = "lower",
# # lab = TRUE,
# # lab_size = 3, insig = 'blank',
# # method="square", p.mat = corr, sig.level = 0.4,
# # colors = c("tomato2", "white", "springgreen3"),
# # title="Correlogram of mtcars",
# # ggtheme=theme_bw) + geom_point(aes(colour = cut(pvalue, c(-Inf, 0.1, 0.2, Inf))),
# # + size = 5) +
# # scale_color_manual(name = "pvalue",
# # values = c("(-Inf,0.1]" = "black",
# # + "(0.1,0.2]" = "yellow",
# # + "(0.2, Inf]" = "red"),
# # labels = c("<= 0.1", "0.1 < pval <= 0.2", "> 0.2"))
# #
#
#
#
#
#
#
#
#
#
#
# #
# # > corr <- matrix(runif(100),nrow=10)
# # > ggcorrplot(corr, hc.order = TRUE,
# # type = "lower",
# # lab = TRUE,
# # lab_size = 3,
# # method="circle",
# # colors = c("tomato2", "white", "springgreen3"),
# # title="Correlogram of mtcars",
# # ggtheme=theme_bw)
# # # myplot_corr
# # # cat(file = stderr(), 'ggcorr\n')
# # # ggcorrplot(mat_p)
# #
# # # nbreaks=8,
# # # use = "everything",
# # # palette='RdGy',
# # # label=TRUE,
# # # label_size=5,
# # # label_color='white')
# # mat_p_sig = mat_p
# # mat_p_sig[mat_p_sig>0.05]=0.05000001
# # # xx<-ggcorr(
# # # data = NULL,
# # # cor_matrix = mat_p_sig,
# # # nbreaks = 5,
# # # label = TRUE,
# # # drop = TRUE,
# # # limits = FALSE #c(0,0.05)
# # # )
# # df <- as.data.frame(mat_p)
# #
# # xx <- ggcorr(
# # data = NULL,
# # cor_matrix = mat_p,
# # geom = "blank",
# # digits = 3,
# # label = TRUE,
# # hjust = 0.75,
# # angle = -45) +
# #
# # geom_point(
# # size = 12,
# # aes(color = coefficient > 0,
# # alpha = abs(coefficient) < 0.05)) +
# # scale_alpha_manual(values = c("TRUE" = 0.25, "FALSE" = 0)) +
# # geom_mark(data = df)+ #, aes(p.value=mat_p))+
# # #geom_abline(slope = -1, intercept = dim(mat_p)-1)+
# # geom_abline(slope = 1, intercept = 0)+
# # guides(color = FALSE, alpha = FALSE)
# #
#
# #xx<- generate_histogram_plot_facet(input$group1, input$group2, input$trial1, input$trial2, freq(), level_x_rval(), level_y_rval())
# return(p)
# }
# if (input$method=="Circle"){
# myplotcircle = generate_plot_Circle(d$mat_p, d$mat_t, d$data1, d$data2)
#
#
# }
# if (input$method=="Pheatmap"){
#
# cur_dev <- dev.cur()
# # Pheatmat setzt das dev.cur() um ... daher manuelles zuruck setzen
# myplotpheatmap = generate_plot_Pheatmap(d$mat_p, d$mat_t, myfontsize = 18)
# #cur_dev <- dev.cur()
# #cat(file = stderr(), paste0("cur_dev=", cur_dev,"\n"))
# dev.set(cur_dev)
# return(myplotpheatmap)
#
# }
#
# }
# )
#
# output$text_bottom <- renderPrint({
# x = curdata()$data1[, level_y_rval(), level_x_rval()]
# y = curdata()$data2[, level_y_rval(), level_x_rval()]
# z = t.test(x,y, paired = curdata()$my_paired)
# out <- create_my_ttest_string(z, paired = curdata()$my_paired, mean1 = mean(x), mean2 = mean(y))
# cat(out)
# })
#
# output$hist <- renderPlot({
#
# generate_histogram_plot_facet(input$group1, input$group2, input$trial1, input$trial2, g_sel_freqs(), level_x_rval(), level_y_rval())
#
# })
#
#
# output$facet <- renderPlot({
# df = tbl_beh
# d = data_freqmean()
# df$data1 = d[,level_x_rval, level_y_rval, input$trial1]
# df$num <- ave(df$data1, df$Gruppe, FUN = seq_along)
#
# })
#
# output$htmlhelp_Comp_Plot <- renderUI({
# # if (showhtml()){
# includeMarkdown(rmarkdown::render("./documentation/comp_plot_markdown.md"))
# # }
# })
#
#
#
#
#
# # Observe Funktion fuer den zentralen Specherbutton
# observeEvent(g_saveImage_button(),{
# req(input$group1)
# req(input$group1)
# req(input$trial1)
# req(input$trial2)
#
# cat(file = stderr(), "observeEvent(g_save_Image_button(), with input$method =", input$method,"\n")
# cat(file = stderr(), "dpi=",g_saveImage_dpi(),"\n")
# d <- curdata()
# #if (g_saveImage_button()>0){
# filename = paste0(g_saveImage_filename(),"_hist", format(Sys.time(), "%Y-%m-%d-%H-%M-%S."), g_saveImage_fileext())
# myplot<-generate_histogram_plot_facet(input$group1, input$group2, input$trial1, input$trial2, g_sel_freqs(), level_x_rval(), level_y_rval())
# ggsave(file = filename, width = g_saveImage_width(), height =g_saveImage_height(), units = "cm", plot = myplot, type = "cairo", dpi = g_saveImage_dpi())
# #}
#
#
# filename2 = paste0(g_saveImage_filename(),"_",input$method, format(Sys.time(), "%Y-%m-%d-%H-%M-%S."), g_saveImage_fileext())
# open_device_for_save(filename2)
# myplot = switch(
# input$method,
# "Corrplot" = generate_plot_Corrplot(d$mat_p, d$mat_t),
# "Circle" = generate_plot_Circle(d$mat_p, d$mat_t, d$data1, d$data2),
# "Pheatmap" = generate_plot_Pheatmap(d$mat_p, d$mat_t)
# )
# dev.off()
# }
# )
#
# observeEvent(input$ExportData, {
# session$sendCustomMessage(type = 'testmessage',
# message = 'saving data now')
# #ggsave(file = "tmpbutton.png")
# #ggsave(plot = x1, filename = "x1plot.png", type = "cairo", dpi = 600)
# req(input$trial1)
# req(input$trial2)
# req(input$group1)
# req(input$group2)
# d <- curdata()
# data1 <- d$data1
# data2 <- d$data2
# string1 <-d$string1
# mat_p <- d$mat_p
# mat_t <- d$mat_t
# saveRDS(mat_p, file = "./exported_variables_from_visualizer/ExportData2D_mat_p.Rds")
# saveRDS(mat_t, file = "./exported_variables_from_visualizer/ExportData2D_mat_t.Rds")
# saveRDS(data1, file = "./exported_variables_from_visualizer/ExportData3D_data1_subj_reg1_reg2.Rds")
# saveRDS(data2, file = "./exported_variables_from_visualizer/ExportData3D_data2_subj_reg1_reg2.Rds")
#
# })
#
# }
# )
# }
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