z0on
commented
3 years ago 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 notifications@github.com 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
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-- cheers Misha matzlab.weebly.com
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.
)
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