gomwuplot error

[Abigailtangtang]

Dear Dr. Matz,
Hi, I tried to run GO_MWU.R on my ThinkPad, but when I tried to plot results some error happened.
The plot was generated successfully but the following steps could not be performed.

`results=gomwuPlot(input,goAnnotations,goDivision,

               absValue=-log(0.05,10),  # genes with the measure value exceeding this will be counted as "good genes". This setting is for signed log-pvalues. Specify absValue=0.001 if you are doing Fisher's exact test for standard GO enrichment or analyzing a WGCNA module (all non-zero genes = "good genes").
               #	absValue=1, # un-remark this if you are using log2-fold changes

               level1=0.1, # FDR threshold for plotting. Specify level1=1 to plot all GO categories containing genes exceeding the absValue.

               level2=0.05, # FDR cutoff to print in regular (not italic) font.
               level3=0.01, # FDR cutoff to print in large bold font.
               txtsize=1.2,    # decrease to fit more on one page, or increase (after rescaling the plot so the tree fits the text) for better "word cloud" effect
               treeHeight=0.5, # height of the hierarchical clustering tree
               #	colors=c("dodgerblue2","firebrick1","skyblue2","lightcoral") # these are default colors, un-remar and change if needed

)

GO terms dispayed: 64
"Good genes" accounted for: 1572 out of 2625 ( 60% )
Warning messages:
1: In plot.formula(c(1:top) ~ c(1:top), type = "n", axes = F, xlab = "", :
the formula 'c(1:top) ~ c(1:top)' is treated as 'c(1:top) ~ 1'
2: In plot.formula(c(1:top) ~ c(1:top), type = "n", axes = F, xlab = "", :
the formula 'c(1:top) ~ c(1:top)' is treated as 'c(1:top) ~ 1'`

The last few lines are the warning messages I got. It happened either I input my data file or the example file you offered. As a consequence, result[[1]] does not work, as well as the following steps.
Could you please give me some suggestions?
Thanks a lot!

Abigail

[z0on]

Hi Abigail - thanks for trying my method! Just making sure: you are trying to run results[[1]] , not result[[1]] like you say in your message? Because this would not work for obvious reason (there is no ‘result’ object) Also - how long ago did you install GO_MWU? (I’ve pushed one not fully tested update yesterday so I wonder if that might be giving trouble) Anyway, let me know if the issue reappears after you completely reload the whole R space. Cheers Misha

On Wed, Dec 23, 2020 at 2:45 AM Abigailtangtang ***@***.***> wrote: Dear Dr. Matz, Hi, I tried to run GO_MWU.R on my ThinkPad, but when I tried to plot results some error happened. The plot was generated successfully but the following steps could not be performed. `results=gomwuPlot(input,goAnnotations,goDivision, absValue=-log(0.05,10), # genes with the measure value exceeding this will be counted as "good genes". This setting is for signed log-pvalues. Specify absValue=0.001 if you are doing Fisher's exact test for standard GO enrichment or analyzing a WGCNA module (all non-zero genes = "good genes"). # absValue=1, # un-remark this if you are using log2-fold changes level1=0.1, # FDR threshold for plotting. Specify level1=1 to plot all GO categories containing genes exceeding the absValue. level2=0.05, # FDR cutoff to print in regular (not italic) font. level3=0.01, # FDR cutoff to print in large bold font. txtsize=1.2, # decrease to fit more on one page, or increase (after rescaling the plot so the tree fits the text) for better "word cloud" effect treeHeight=0.5, # height of the hierarchical clustering tree # colors=c("dodgerblue2","firebrick1","skyblue2","lightcoral") # these are default colors, un-remar and change if needed ) GO terms dispayed: 64 "Good genes" accounted for: 1572 out of 2625 ( 60% ) Warning messages: 1: In plot.formula(c(1:top) ~ c(1:top), type = "n", axes = F, xlab = "", : the formula 'c(1:top) ~ c(1:top)' is treated as 'c(1:top) ~ 1' 2: In plot.formula(c(1:top) ~ c(1:top), type = "n", axes = F, xlab = "", : the formula 'c(1:top) ~ c(1:top)' is treated as 'c(1:top) ~ 1'` The last few lines are the warning messages I got. It happened either I input my data file or the example file you offered. As a consequence, result[[1]] does not work, as well as the following steps. Could you please give me some suggestions? Thanks a lot! Abigail — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#8>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZUHGBRVLNQUIQSNL7RD4TSWGU2NANCNFSM4VGWUMSA> .

-- cheers Misha matzlab.weebly.com

[Abigailtangtang]

Dear Misha,
Thanks for your reply!
Sorry, that was a typing mistake. Actually, I copied and pasted results[[1]] from GO_MWU.R to run in RStudio.
I noticed that you have updated the script and I have tried both, but this warning message always appeared.

Best wishes
Abigail

[z0on]

hmmm. Which R version are you running?

…

On Wed, Dec 23, 2020 at 7:42 PM Abigailtangtang ***@***.***> wrote: Dear Misha, Thanks for your reply! Sorry, that was a typing mistake. Actually, I copied and pasted results[[1]] from GO_MWU.R to run in RStudio. I noticed that you have updated the script and I have tried both, but this warning message always appeared. Best wishes Abigail — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZUHGCOF6RTO5D7KZ2LWBTSWKMBLANCNFSM4VGWUMSA> .

[Abigailtangtang]

Oh, maybe that is the point! I updated the R and it works well now.
Thanks a lot for providing such a good package!

[z0on]

Whew! You got me worried for a moment :) Do let me know if you have any questions! Happy holidays!

On Wed, Dec 23, 2020 at 9:26 PM Abigailtangtang ***@***.***> wrote: Oh, maybe that is the point! I updated the R and it works well now. Thanks a lot for providing such a good package! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZUHGCFX7MCRPDA2C4INJLSWKYFJANCNFSM4VGWUMSA> .

-- cheers Misha matzlab.weebly.com

[Abigailtangtang]

I am sorry for that. Thanks so much!
Merry Christmas!

Abigail

[z0on]

nothing to be sorry about! thank *you* so much for testing my crappy code :) Misha

…

On Fri, Dec 25, 2020 at 9:35 PM Abigailtangtang ***@***.***> wrote: I am sorry for that. Thanks so much! Merry Christmas! Abigail — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZUHGGSZCFAOYYX4LWRAR3SWVKY7ANCNFSM4VGWUMSA> .