My R was installed in a conda environment on Ubuntu 20.04.1 VM.
I was searching for this problem when i found this thread. I too am using RStudio from Anaconda, on Debian 10.0 (buster).
Try
par(family = "Arial")
or whichever font name before calling plot(). It worked for me.
Update > I still had problems with ggplot2 plots not displaying labels, like above. I tried the workaround of using showtext() instead of regular text rendering.
install.packages("showtext")
After it was installed,
library(showtext)
to load the library. Then simply call
showtext_auto()
followed by the ggplot(.....) + ... + etc. function and text was rendered alright within the plot. I did not load specific fonts using font_add(). Maybe because previously 'Arial' was loaded with par()
Related
I'm using an M1, Big Sur Macbook. I need to embed the fonts of a number of pdfs that include plots from ggplot2.
However, when I run the embed_fonts() function, it returns the following error message: GhostScript was not found
With Homebrew, I installed Ghostscript. I have also reinstalled extrafont and extrafontdb, restarted RStudio, and then run font_import() and loadfonts() again. None of this solves the error message.
Have you experienced this problem? I wonder if it's because of the change to the M1's Apple Silicon?
I have also switched from using bash to zsh in my terminal. Could that have affected this?
A reprex:
library(ggplot2)
library(extrafont)
(plot <- ggplot(cars, aes(x = speed, y = dist)) +
geom_point())
ggsave("test_plot.pdf", plot)
embed_fonts(file = "test_plot.pdf", outfile = "test_plot_embedded.pdf")
I found the following two answers that seem related, but I'm unsure how to implement them:
How to fix "Unable to find GhostScript executable to run checks on size reduction" error upon package check in R?
R does not recognize GhostScript to embed eps plots
My issue was solved when I installed Ghostscript directly https://pages.uoregon.edu/koch/ (Ghostscript 9.54.0)
It appears there was, at least on my end, an issue using homebrew install ghostscript. When I ran that in Terminal, everything appeared to be fine. No error messages.
As you can see in this post someone found the solution to my problem where the text in my ggplot2 graphs were replaced by unicode-blocks. This was caused by an error in the default font settings of ggplot2 (base_family = ""). Therefore, the workaround was to manually set the base_family argument to "Arial".
Here you can see an example code:
# Libraries
library(ggplot2)
# create data
xValue <- 1:10
yValue <- cumsum(rnorm(10))
data <- data.frame(xValue,yValue)
# Plot
ggplot(data, aes(x=xValue, y=yValue)) +
geom_line() +
theme_classic()
The resulting graph looks like this where the text is shown in weird unicode blocks (sorry I do not know what these are called exactly):
I can manually solve the issue by setting the theme base_family to "Arial":
# Libraries
library(ggplot2)
# create data
set.seed(42)
xValue <- 1:10
yValue <- cumsum(rnorm(10))
data <- data.frame(xValue,yValue)
# Plot
ggplot(data, aes(x=xValue, y=yValue)) +
geom_line() +
theme_classic(base_family = "Arial")
This is the image of the resolved issue, which only works if the base_family is set to a specific font like "Arial":
The question is why does my system somehow conflict with the default font and how can I set the default font back to normal? Because now I have to call the base_family = "Arial" Argument in every plot I make with ggplot2. I should mention, that I have no font issues with e.g. plotly whatsoever. I have not found any similar problems except a link on how to change the default setting for a specific theme type but I would like to reset the settings back to normal so base_family = "" works again. I hope you can help me out and please do not hesitate if you need further information from me.
R version: 3.6.1 (2019-07-05)
platform: linux mint x86_64
conda environment
Thanks to #tjebo I was able to resolve the issue by upgrading my R version to 4.0.3. and switched to ipython notebook since as far as I understood R-Studio does not support version 4.0.3 (EDIT: probably only an issue caused by conda and not by R-Studio).
I work with conda and therefore I created a new environment
# Create and activate conda environment
conda create --name r4
conda activate r4
Then I installed the R Verison 4:
# install R version 4
conda install -c conda-forge r-base
conda install -c conda-forge/label/gcc7 r-base
Finally, I installed irkernel in order work with R in IPython notebooks:
# Install R kernel for IPython notebook
conda install -c r r-irkernel
IRkernel::installspec()
# open jupyter notebook
ipython notebook
Inside the ipythone notebook I could now choose "R" as a kernel and the code I previously had issues with works as expected. Again credits to #tjebo.
EDIT: Reinstalling R lead to further issues where packages were not beeing installed correctly due to missing lib files. But this is offtopic so I will probably open another discussion somewhere else. (FYI Link to the solution was postet by #fredaas here)
My R was installed in a conda environment on Ubuntu 20.04.1 VM.
I was searching for this problem when i found this thread. I too am using RStudio from Anaconda, on Debian 10.0 (buster).
Try
par(family = "Arial")
or whichever font name before calling plot(). It worked for me.
Update > I still had problems with ggplot2 plots not displaying labels, like above. I tried the workaround of using showtext() instead of regular text rendering.
install.packages("showtext")
After it was installed,
library(showtext)
to load the library. Then simply call
showtext_auto()
followed by the ggplot(.....) + ... + etc. function and text was rendered alright within the plot. I did not load specific fonts using font_add(). Maybe because previously 'Arial' was loaded with par()
When I generate any ggplot2 plot using R magic in Jupyter Notebook, all text in the plot is rendered as little empty boxes.
My environment is running the notebook via Jupyter Hub on Ubuntu server. R magic is working great in general, with the goal of re-using some existing R code I have to output a Word Cloud via wordcloud package. However, when I generate any plot using ggplot2 any text is missing and all I see are small empty boxes.
library(ggplot2)
ggplot(mtcars, aes(x = drat, y = mpg)) +
geom_point()
see image here
The plot should show text on the axis labels but no text is displayed, just empty boxes.
Generating the same plot when running R from ssh terminal and saving it to disk (it's on a headless server) looks fine. Generating plot via pandas data frame in a different cell looks fine. So it seems related to rpy2? I'm stumped.
[EDIT]: in fact I see the same behavior using R kernel on this server, so it seems to not be specific to rpy2 / R magic.
I was able to solve this by installing all the needed packages via R install.packages() rather than conda. Next time I think I will avoid using conda for R packages altogether; this isn't the first time it has caused issues.
When I run my code all my graphs (both ggplot2 and plot) are displayed in an external "Quartz 2 [*]" graphical viewer.
I would like them to be displayed in the R studio GUI plot area to I can better save and view my files, along with the previous versions.
Is there anyway to stop this?
I recently updated my version of R, along with the X11 and xQuartz on my mac (also up to date), and I am guessing these updates are behind it.
I have seen many forums explaining how to get rstudio to export to an external viewer (e.g. "quartz()"), but not the other way.
I have looked, but these threads have not helped:
ggplot plots in scripts do not display in Rstudio
plot panel does not produce plots Rstudio
dev.off() even when hidden hide <- dev.off() is not working either.
Any help would be great,
Thanks.
If you upgrade R without upgrading RStudio, the graphics engine may not be compatible. To fix the "Quartz 2" popout, upgrade RStudio to a newer version that supports the graphics engine in the version of R you have installed.
I had the same problem, and noticed the following output to the console:
Warning message:
R graphics engine version 15 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.
Looks like I forgot to reinstall Rstudio as well.. That sorted my problem.