Grouped plots in R

Question

I'm trying to plot a merged plot for bonferroni p adjusted value using ggplot.

I'm running this code

p <- ggplot(stack, aes(x = factor(phenotypes), y = values)) + 
    geom_boxplot(aes(fill = factor(modules))) + 
    theme_prism() + 
    theme(legend.position = "none")

Everytime I run the I get the similar classic error.

Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
  polygon edge not found

The usual problem is font not being presnt in the correct directory. But that doesn't seem to be the issue here.

I'm using this website for reference

EDIT: This is the data, i.e. the "stack" dataset I'm working on.

dput(stack[1:171,])

structure(list(phenotypes = c("Proneural", "Mesenchymal", "Classical", 
"Classical", "Proneural", "Proneural", "Proneural", "Classical", 
"Classical", "Classical", "Proneural", "Mesenchymal", "Proneural", 
"Classical", "Proneural", "Mesenchymal", "Mesenchymal", "Classical", 
"Mesenchymal", "Classical", "Proneural", "Proneural", "Proneural", 
"Mesenchymal", "Mesenchymal", "Mesenchymal", "Mesenchymal", "Proneural", 
"Mesenchymal", "Proneural", "Classical", "Proneural", "Mesenchymal", 
"Mesenchymal", "Proneural", "Proneural", "Mesenchymal", "Mesenchymal", 
"Proneural", "Neural", "Mesenchymal", "Classical", "Proneural", 
"Mesenchymal", "Mesenchymal", "Mesenchymal", "Neural", "Proneural", 
"Neural", "Classical", "Classical", "Proneural", "Classical", 
"Classical", "Classical", "Classical", "Proneural", "Proneural", 
"Mesenchymal", "Classical", "Mesenchymal", "Proneural", "Proneural", 
"Classical", "Classical", "Proneural", "Proneural", "Proneural", 
"Proneural", "Neural", "Mesenchymal", "Mesenchymal", "Classical", 
"Classical", "Proneural", "Proneural", "Mesenchymal", "Neural", 
"Neural", "Classical", "Neural", "Mesenchymal", "Mesenchymal", 
"Classical", "Proneural", "Mesenchymal", "Classical", "Mesenchymal", 
"Mesenchymal", "Mesenchymal", "Proneural", "Neural", "Neural", 
"Mesenchymal", "Proneural", "Neural", "Neural", "Neural", "Proneural", 
"Mesenchymal", "Mesenchymal", "Proneural", "Neural", "Neural", 
"Mesenchymal", "Neural", "Classical", "Mesenchymal", "Mesenchymal", 
"Mesenchymal", "Neural", "Mesenchymal", "Neural", "Mesenchymal", 
"Classical", "Neural", "Neural", "Neural", "Neural", "Proneural", 
"Neural", "Proneural", "Mesenchymal", "Classical", "Mesenchymal", 
"Proneural", "Mesenchymal", "Proneural", "Proneural", "Mesenchymal", 
"Mesenchymal", "Proneural", "Proneural", "Proneural", "Classical", 
"Proneural", "Mesenchymal", "Proneural", "Proneural", "Neural", 
"Proneural", "Mesenchymal", "Proneural", "Classical", "Classical", 
"Classical", "Classical", "Proneural", "Mesenchymal", "Classical", 
"Neural", "Proneural", "Neural", "Mesenchymal", "Mesenchymal", 
"Mesenchymal", "Mesenchymal", "Classical", "Mesenchymal", "Classical", 
"Proneural", "Classical", "Neural", "Mesenchymal", "Proneural", 
"Classical", "Classical", "Proneural", "Proneural", "Mesenchymal", 
"Mesenchymal"), values = c(-0.126482404651362, 0.00859685106988051, 
-0.139119978025995, -0.121760256216002, -0.114050357589663, -0.16158166178197, 
-0.169089521235389, 0.134388350128016, -0.128728040505512, 0.0933639502568886, 
-0.116285533417, -0.0715164710720025, -0.050281653395796, -0.0712583935347317, 
-0.116848802717176, -0.1394796603133, -0.131958454866075, -0.167862157710569, 
0.0781961256653059, -0.0874083890994826, -0.142602528126273, 
-0.132749359004561, 0.0530754944359762, -0.112556115187184, -0.126475329197849, 
-0.103764754820242, -0.0377897554734426, -0.0825700087419535, 
0.0565802594387166, -0.127113477946288, 0.0621406527851034, -0.0353373248499261, 
0.0651104404770428, -0.046842885259204, -0.0388244031159389, 
-0.0331569959442778, 0.033701438947606, 0.0642070914755685, -0.0753508936454846, 
0.116575055033346, 0.0618127428574358, 0.0913128306164853, -0.131098598718593, 
0.00663000043165442, 0.087646298412118, 0.0424501375261861, 0.132271826019638, 
-0.116098261441119, 0.150578014972223, 0.0370869606412521, 0.124207975834675, 
-0.0697137156198783, 0.045603425091438, 0.128723238203833, -0.00899840307387745, 
0.0716898207350761, 0.0278474335783047, -0.00251548498551291, 
0.00944990607573422, 0.063040030569466, -0.00966936428286957, 
-0.103167359695479, -0.109970747377413, 0.092822101720664, 0.0599647788263245, 
-0.0402260247392427, 0.0561493322564905, -0.0337741476357838, 
0.0123028680258031, 0.0829652405103008, 0.0473861745713383, 0.0552591953919883, 
0.0589190391293063, 0.0542800207749991, -0.0590957568660261, 
-0.0768057537931389, -0.0631594939938725, 0.0232166721127454, 
0.0794818086402467, 0.0163758735536393, 0.0364047314888439, -0.056987419443193, 
0.0102418241805152, 0.0834466785300582, -0.0621321025318891, 
-0.0202384484936535, 0.0472178852980202, 0.0500099068565177, 
-0.000386746443747292, 0.0336169099739554, -0.0196318551702082, 
0.0215504671153622, 0.0370043737532354, 0.00236114001435378, 
0.0187774063941158, 0.0118748174856794, 0.0438428539755876, 0.0590938337833555, 
-0.0214051371142639, 0.048970263838942, -0.0353986999749805, 
-0.0652888103586655, 0.0307980036631203, 0.0435024586638615, 
0.06349210003803, 0.0699162740441559, 0.0866779470756711, 0.0302570428387929, 
0.039907529282083, 0.0413550598629916, 0.0194677506824577, 0.0382215014456658, 
0.0998571537054834, 0.0249023251158023, 0.0491338848762949, 0.0739696647120266, 
-0.0156915725176812, -0.086181923772576, 0.0484264963060224, 
-0.0952872280628109, -0.0496917131983185, -0.0626613426906559, 
-0.0235720315114444, 0.0402051758624549, 0.0541716193143272, 
-0.0447085228859518, 0.0851145904041888, -0.0750319738540656, 
-0.0395468309394087, -0.0171796695631005, 0.0143116629560395, 
0.0139348413765643, -0.0605286733223814, -0.0680551202279635, 
0.0935675698428226, -0.121323835109815, 0.0650088114184009, 0.0286512581822918, 
-0.0267822397048852, 0.0560594126094381, -0.0866917309227976, 
0.0761270963342822, 0.0102442673059245, 0.064812961280754, 0.0566119307303998, 
0.0903385384522695, -0.0471706176728432, 0.00751391691722696, 
0.0350567757887319, 0.0587473888278628, 0.0645068776643195, -0.0843968892218576, 
0.0978188183251172, -0.0248768078605493, -0.101713696034819, 
0.0535916907441913, 0.081542193680387, 0.107977971088651, 0.076239889269626, 
0.0817493803790159, -0.00988348985129774, 0.119297845556547, 
0.0769790743428255, -0.0632279011942837, -0.140594814112487, 
0.0982145914982851, 0.129445220757845, -0.0740271756065673, -0.049940713932579, 
-0.0076347504220374, 0.00346005068662671), modules = structure(c(1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("MEdarkturquoise", 
"MEtan", "MEdarkgrey", "MEsalmon", "MEviolet", "MEdarkolivegreen", 
"MEdarkred", "MEskyblue", "MEskyblue3", "MEsteelblue", "MEmidnightblue", 
"MEcyan", "MEsienna3", "MEyellowgreen", "MElightcyan", "MEorange", 
"MEblack", "MEdarkmagenta", "MEdarkorange", "MEwhite", "MEblue", 
"MEgrey60", "MEdarkgreen", "MEred", "MEgrey"), class = "factor")), row.names = c(NA, 
171L), class = "data.frame")

It has a total of 4275 rows and 3 columns.

Suggestions shall be welcomed.

Can you share a little bit of data to make your question reproducible? Something like `dput(stack[1:20, ])` will give a copy/pasteable version of the first 20 rows including all class and structure information. Choose a suitable small subset of your data to demonstrate the problem. — Gregor Thomas, May 15 '22 at 21:32
Also, since you've linked to the `ggprism` vignette, can you confirm that the examples there work for you? — Gregor Thomas, May 15 '22 at 21:34
It would help people answer the question if you give them the data (or a small subset of it) so they can reproduce the problem. You can use `dput(stack)` and paste the output into your question, or even better make self sufficient code including all the prerequisites to run it such as the `library()` commands and use the [`reprex` package](https://reprex.tidyverse.org/) — Prashant Bharadwaj, May 15 '22 at 21:36
@PrashantBharadwaj thank you so much for the advice will keep that in mind for the next time. Can you please take a look at it once again as the edits have been made. — driver, May 15 '22 at 23:24
Pictures of data are not very helpful--we can't run your code on a picture, not can we try a solution on a picture. Could you please try using `dput()` to share a small sample of data as both I have Prashant have requested? If you need more guidance on making reproducible examples [we have a FAQ for that](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). If we can't reproduce your error, there is little we can do to help solve it. — Gregor Thomas, May 16 '22 at 00:36
I searched your error message and a couple of links suggest that it could be a font problem, and also try re-running your ggplot code after restarting Rstudio once - [stackoverflow](https://stackoverflow.com/questions/10581440/error-in-grid-calll-textbounds-as-graphicsannotxlabel-xx-xy-polygon) ; [Rstudio community page](https://community.rstudio.com/t/comeback-of-the-infamous-error-in-grid-call-c-textbounds-as-graphicsannot-x-label-x-x-x-y-polygon-edge-not-found-bug/54555/2) — Prashant Bharadwaj, May 16 '22 at 06:00
@PrashantBharadwaj the font seems to be fine. I use macOSMonterey, version 12.3.1 Also the error doesn't specify which font is giving the problem so how can we understand the reason of this problem? — driver, May 16 '22 at 06:06
@GregorThomas Many thanks. I've now added the dataset as you asked for. Suggestions shall be welcomed — driver, May 16 '22 at 06:08

score 1 · Accepted Answer · answered May 16 '22 at 23:31

1

I'm unable to reproduce your error, with the 171 row data you gave, I got this plot

Like I mentioned in the comment, the bug might be gone once you restarted Rstudio. Check if you are still getting the error and try these pages - stackoverflow ; Rstudio community page

answered May 16 '22 at 23:31

Prashant Bharadwaj

375
1
9

Thanks, restarting worked for me. After every few iterations, this problem did turn up but restating solves it each time. – driver May 18 '22 at 17:40

Grouped plots in R

1 Answers1