how can I change the default jpeg() export quality via console in R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"?
Here is an example: jpeg('../data/all/graphic1.jpg', quality=100)
But I don't want to change all separate jpeg() command...
Thanks for your help
You could define a new function that over-rides the default function with a version such as:
jpeg <- function(filename, quality=100, ...) grDevices::jpeg(filename, quality, ...)
This would work for most common situations where the jpeg function is used (say in a user script), but may not work correctly when the jpeg function is being called from within functions in other packages.
Related
]
2
I was not able to get a batch of images with tiff() R function inside for loop.
I have x86_64-w64-mingw32/x64 (64-bit) platform with installed Windows 8.1 and RStudio Version 1.0.143 with R version 3.6.0 (2019-04-26) -- "Planting of a Tree". I tried to obtaine a batch of tiff images by putting my code inside the for loop. Unfortunately that resulted in the numerous broken files (in attachment). But if i type exactly the same code in the RStudio console i got normal (valid) image.
#Fragment of the script
for (i in 1:nrow(BH))
{
...
tiff( paste(pos$rs[1],"tiff",sep = '.'))
ggplot(df_g_,aes(x=factor(g),fill=factor(O)))+geom_bar(stat="count")+xlab("")+labs(fill='')
dev.off()
}
#If i perform the following code in console after script execution i got a valid image
tiff( paste(pos$rs[1],"tiff",sep = '.'))
ggplot(df_g_,aes(x=factor(g),fill=factor(O)))+geom_bar(stat="count")+xlab("")+labs(fill='')
dev.off()
The solution was to envelop ggplotfunction by base print function in the loop:
print(ggplot(df_g_,aes(x=factor(g),fill=factor(O)))+geom_bar(stat="count")+xlab("")+labs(fill=''))
So, i've used the solution from the other post:
enter link description here
Consider a minimal example: generating an empty plot with ggplot2 and put it into a PDF file. Typically people would do
pdf()
ggplot()
dev.off()
and it works as expected. However, when you wrap these statements into an if-statement, the resulting PDF file becomes corrupted.
if (TRUE) {
pdf()
ggplot()
dev.off()
}
This issue has been reproduced on both Windows 10 and macOS Mojave. I'm using the latest version of R
$ R --version
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin18.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.
To save a ggplot object using pdf or jpg functions, one has to explicitly print the ggplot.
if (TRUE) {
pdf()
print(ggplot())
dev.off()
}
This is stated in R-FAQ 7.22 Why do lattice/trellis graphics not work?
The most likely reason is that you forgot to tell R to display the graph. Lattice functions
such as xyplot() create a graph object, but do not display it (the
same is true of ggplot2 graphics, and Trellis graphics in S-PLUS). The
print() method for the graph object produces the actual display. When
you use these functions interactively at the command line, the result
is automatically printed, but in source() or inside your own functions
you will need an explicit print() statement.
So, it would not save if one simply source a script even in the absence of a conditional statement or loop (source with echo = TRUE would save the plot).
I personally prefer to use the ggsave function since it seems more flexible.
if (TRUE) {
ggplot()
ggave(filename = "plot.pdf")
}
how to make knitr use the same R session in RStudio?
FYI, I am working a huge amount of data (7 GB of RAM used by the R session) and I do not want to avoid having to use load('data.RData')
Update
Knitr uses a new R session while running the .Rmd. Consequently, all my R objects can not be found. That's why I have to used the function load('mydata.RData')
Thanks
In case you use .Rnw files type directly in the console (given the working directory is where your file resides):
knitr::knit("filename.Rnw")
# or
knitr::knit2pdf("filename.Rnw")
The later also converts filename.tex to filename.pdf
For classical .Rmd files you can use the same
knitr::knit("filename.Rmd")
# or
knitr::knit2html("filname.Rmd")
For the newer workflow using rmarkdown package use
rmarkdown::render("filename.Rmd")
This works because by default the knit and render functions have the envir argument set to envir=parent.frame(), which is usually the global environment of your R-Session.
Calling knit or render by clicking the knit button in R-Studio on the other hand calls these functions with argument envir=new.env().
I have followed this blog to customize base R plot font on macOS (using quartzFonts() in .Rprofile), with success to a certain degree. My problem with this approach is, defining a new font family has to be put in a function such as .define.fonts() and upon enter a R session (I use Rstudio), I have to manually invoke the following from the console:
.define.fonts()
par(family='new_font_family')
I can't simply define new font family by calling quartzFonts() in .Rprofile. My guess is that this command is not available until graphic device has been initialized. Is there anyway to automate this?
From #DWin and #Ben Bolker, we can change the scatter3d function in R to plot "prettier" (http://stackoverflow.com/questions/8204972/carscatter3d-in-r-labeling-axis-better), however, saving the plot is a trickier. rgl.snapshot saves the image as a png but to save a high resolution image (PDF) rgl.postscript must be used. Using rgl.postscript will not save the image with font/text size/axis sizes as specified (I edited the scatter3d function to increase text/axis sizes). rgl.snapshot works as it should so why doesn't rgl.postscript? Does anyone know an alternative saving method or is there a way to save the plot with larger text/axis etc?
A simple example works for me with the a more recent version of rgl than the CRAN one (CRAN has 0.92.798, r-forge now has 0.92.836, this is with 0.92.829). It looks like versions are numbered by SVN revision, so this is one version after the update mentioned in the comments above ...
library(rgl)
set.seed(1001)
n <- 20
text3d(runif(n),runif(n),runif(n),LETTERS[1:n],cex=seq(0.5,5,length=n))
rgl.postscript(file="tmp.ps")
However, a big warning is that the resulting PS, PDF, files etc. are a bit wonky. The bounding boxes are a little odd, although I could text-edit that manually. ps2pdf and ps2png mangled it .. epstopdf seems to have worked (these are all tools that are available on Linux boxes, don't know about for other OS). In principle rgl.postscript() allows you to export as PDF, but it might be weird PDF ... StackOverflow doesn't recognize the file as being in a valid upload format.
R Under development (unstable) (2012-01-01 r58032)
Platform: i686-pc-linux-gnu (32-bit)
[snip]
other attached packages:
[1] rgl_0.92.829