I have been using R and RStudio with base and ggplot for a couple of years. Lately, it seems that when some plots are generated, other plots are lost/deleted.
In RStudio, I use the "Plots" pane/tab, and the blue left and right arrows to view the plots that have been created. By disappears, I mean a plot was created and visible here, but if I use the arrows, I can't see it anymore. It was there, and it is not there anymore, it has "disappeared".
After running the code below using "Source" button, which does 3 plots, I can only see 2 plots. If I step through the code using Command-Return, I see the 3 plots generated, but then the middle one gets lost.
After doing more testing, I see for this code it is the call to:
DataExplorer::plot_str(mtcars)
that is the problem. If I comment that line and use another plot from DataExplorer like:
DataExplorer::plot_intro(mtcars)
all the plots are available after the script is complete.
I believe everything is using the latest versions:
- mac os - 11.5.2
- R - R version 4.1.1 (2021-08-10)
- RStudio - RStudio 2021.09.0 351
- R libraries - have just updated all the r libraries
Here is a simple base case that seems to recreate the issue. In the example below I am using the DataExplorer library, but I get similar stuff happening in Keras.
Code
########################### Start Initialisation ########################################################################################
# Remove objects from environment
rm(list = ls())
# Clear the R studio console
cat("\014")
# Clear all plots in R studio
try(dev.off(dev.list()["RStudioGD"]),silent<-TRUE)
try(dev.off(),silent<-TRUE)
# Load packages, installing first if not already installed
if (!require(DataExplorer)) {
install.packages("DataExplorer")
library(DataExplorer)
}
##################################
# Use base plotting to plot iris, this works
base::plot(iris, main="iris 1")
# Use DataExplorer::plot_str() to plot mtcars, this works, but then disappears
data("mtcars")
# DataExplorer::plot_str(mtcars) # This causes the problem
DataExplorer::plot_intro(mtcars) # This works
# This plot appears, but seems to cause the one above "mtcars" to disappear
base::plot(iris, main="iris 2")
sessionInfo()
Output:
> # Clear all plots in R studio
> try(dev.off(dev.list()["RStudioGD"]),silent<-TRUE)
null device
1
> try(dev.off(),silent<-TRUE)
> # Load packages, installing first if not already installed
> if (!require(DataExplorer)) {
install.packages("DataExplorer")
library(DataExpl .... [TRUNCATED]
> ##################################
>
> # Use base plotting to plot iris, this works
> base::plot(iris, main="iris 1")
> # Use DataExplorer::plot_str() to plot mtcars, this works, but then disappears
> data("mtcars")
> DataExplorer::plot_str(mtcars)
> # This plot appears but seems to cause the one above "mtcars" to disappear
> base::plot(iris, main="iris 2")
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.5.2
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DataExplorer_0.8.2
loaded via a namespace (and not attached):
[1] pillar_1.6.3 compiler_4.1.1 tools_4.1.1 digest_0.6.28 jsonlite_1.7.2 evaluate_0.14 lifecycle_1.0.1 tibble_3.1.4 gtable_0.3.0 pkgconfig_2.0.3
[11] rlang_0.4.11 igraph_1.2.6 DBI_1.1.1 yaml_2.2.1 parallel_4.1.1 xfun_0.26 fastmap_1.1.0 gridExtra_2.3 dplyr_1.0.7 knitr_1.36
[21] generics_0.1.0 vctrs_0.3.8 htmlwidgets_1.5.4 grid_4.1.1 tidyselect_1.1.1 glue_1.4.2 data.table_1.14.2 R6_2.5.1 fansi_0.5.0 rmarkdown_2.11
[31] ggplot2_3.3.5 purrr_0.3.4 magrittr_2.0.1 scales_1.1.1 ellipsis_0.3.2 htmltools_0.5.2 networkD3_0.4 assertthat_0.2.1 colorspace_2.0-2 utf8_1.2.2
[41] munsell_0.5.0 crayon_1.4.1
I thought perhaps the issue was due to mixing different plotting libraries, but the code below which draws 6 plots, 3 using base:plot() and 3 using ggplot2::ggplot() works and generates 6 plots that I can navigate through in RStudio using the blue left and right arrow buttons on the "Plots" pane/tab.
base::plot(mpg, main="mpg 1 - base")
ggplot2::ggplot(mpg, aes(displ, hwy, colour = class))
geom_point()
ggtitle("mpg 1 - ggplot2")
base::plot(ToothGrowth, main="ToothGrowth 2 - base")
ggplot2::ggplot(ToothGrowth, aes(x=supp, y=len, fill=dose))
geom_boxplot()
ggtitle("ToothGrowth 2 - ggplot2")
base::plot(iris, main="iris 3 - base")
ggplot2::ggplot(iris, aes(x=Sepal.Length, y=Sepal.Width, fill=Species))
geom_boxplot()
ggtitle("iris 3 - ggplot2")
RStudio is:
RStudio 2021.09.0 351 "Ghost Orchid" Release (077589bcad3467ae79f318afe8641a1899a51606, 2021-09-20) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 11_5_2) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
Mac os version:
(base) % uname -a
Darwin xxxx.lan 20.6.0 Darwin Kernel Version 20.6.0: Wed Jun 23 00:26:31 PDT 2021; root:xnu-7195.141.2~5/RELEASE_X86_64 x86_64
(base) % sw_vers
ProductName: macOS
ProductVersion: 11.5.2
BuildVersion: 20G95
CodePudding user response：
I think the reason is a simple one: you're not outputting a real plot (static).
DataExplorer::plot_intro(mtcars) is the problematic "plot" and the underlying code for this includes diagonalNetwork towards the end of the function:
DataExplorer
function (data, type = c("diagonal", "radial"), max_level = NULL,
print_network = TRUE, ...)
{
i <- idx <- parent <- NULL
str_output_raw <- capture.output(str(data, vec.len = 0, give.attr = FALSE,
give.length = FALSE, list.len = 2000000000L))
str_output <- unlist(lapply(str_output_raw, function(x) {
gsub(" \\.{2}\\@", "\\$\\@", x)
}))
n <- length(str_output)
base_split <- tstrsplit(str_output[2:n], "\\$")
nest_level <- (nchar(base_split[[1]]) - nchar(gsub(" \\.{2}",
"", base_split[[1]])))/3 1
diff_nl <- diff(nest_level)
s4_start_index <- which(diff_nl > 1L) 1L
if (length(s4_start_index) > 0) {
s4_end_index <- which(diff_nl == -2L)
s4_index_range <- unique(unlist(lapply(s4_start_index,
function(i) {
seq.int(i, s4_end_index[which.min(abs(s4_end_index -
i))])
})))
nest_level[s4_index_range] <- nest_level[s4_index_range] -
1L
}
if (is.null(max_level)) {
max_level <- max(nest_level)
}
else if (max_level <= 0 | max_level > max(nest_level)) {
stop(paste0("max_level should be between 1 and ",
max(nest_level)))
}
else {
max_level <- max_level
}
comp_split <- tstrsplit(base_split[[2]], ":")
comp_root <- gsub(" ", "", comp_split[[1]])
comp_root[which(comp_root == "")] <- make.names(comp_root[which(comp_root ==
"")], unique = TRUE)
if (anyDuplicated(comp_root))
comp_root[which(duplicated(comp_root))] <- make.names(comp_root[which(duplicated(comp_root))],
unique = TRUE)
comp_output <- paste0(comp_root, " (", trimws(gsub("NULL|\\.{3}|\\.{2}",
"", comp_split[[2]])), ")")
str_dt <- data.table(idx = seq_along(nest_level), nest_level,
parent = comp_output)[nest_level <= max_level]
str_dt <- str_dt[str_dt[, list(i = idx, nest_level = nest_level -
1, child = parent)], on = list(nest_level, idx < i),
mult = "last"]
drop_columns(str_dt[is.na(parent), `:=`(parent, paste0("root (",
str_output[1], ")"))], c("idx", "nest_level"))
str_to_list <- function(str_dt, root_name = as.character(str_dt[["parent"]][1])) {
str_list <- list(name = root_name)
children <- str_dt[parent == root_name][["child"]]
if (length(children) > 0) {
str_list[["children"]] <- lapply(children,
str_to_list, str_dt = str_dt)
}
str_list
}
str_list <- str_to_list(str_dt)
if (print_network) {
type <- match.arg(type)
if (type == "diagonal")
print(diagonalNetwork(str_list, ...))
if (type == "radial")
print(radialNetwork(str_list, ...))
}
invisible(str_list)
}
where diagonalNetwork uses htmlwidgets:
function (List, height = NULL, width = NULL, fontSize = 10, fontFamily = "serif",
linkColour = "#ccc", nodeColour = "#fff", nodeStroke = "steelblue",
textColour = "#111", opacity = 0.9, margin = NULL)
{
if (!is.list(List))
stop("List must be a list object.")
root <- List
margin <- margin_handler(margin)
options = list(height = height, width = width, fontSize = fontSize,
fontFamily = fontFamily, linkColour = linkColour, nodeColour = nodeColour,
nodeStroke = nodeStroke, textColour = textColour, margin = margin,
opacity = opacity)
htmlwidgets::createWidget(name = "diagonalNetwork",
x = list(root = root, options = options), width = width,
height = height, htmlwidgets::sizingPolicy(padding = 10,
browser.fill = TRUE), package = "networkD3")
}
htmlwidgets is an interactive "plot" and opens under RStudio's viewer pane and not the static plots pane.