ReactomePA / Reactome: Crash when plotting
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@martinbusch-15897
Last seen 16 months ago

Hi everybody,

ReactomePA used to work fine in my handy, however, when trying to plot results it recently started to crash Rstudio completely. I cannot see an appearent reason, e.g. I can dotplot a result, but using emapplot of the same result one line of code later it completely crashes. Ocassionally I can perform two plots (dotplot and emapplot) of one dataset, but when using the next one it starts to crash again. Is there any known issue? as.data.frame(result) always works nicely and displays resulting terms... it seems a bit random. Any ideas on how to track down the bug? Any help appreciated - thank you in advance!

Best,

Martin

reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome • 725 views
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pls make sure you are using latest release version.

 

If the issue still exists when using latest release version, pls provide reproducible example.

 

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Thank your for getting in touch. The version I am using is 1.24.0. An example would be the following:

rm(list=ls())
library(ReactomePA)

dataSets <- c("http://martin-busch.com/work/set1.csv",
              "http://martin-busch.com/work/set2.csv",
              "http://martin-busch.com/work/set3.csv",
              "http://martin-busch.com/work/set4.csv"
)

for (dataSet in dataSets) {
      data <- read.table(dataSet, header=T)
      result <- enrichPathway(data$x, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2)
      
      dotplot(result)
      emapplot(result, color = "pvalue")
}

# Manual
dataSet <- dataSets[1]

data <- read.table(dataSet, header=T)
result <- enrichPathway(data$x, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2)

dotplot(result)
emapplot(result, color = "pvalue")

dataSet <- dataSets[2]

data <- read.table(dataSet, header=T)
result <- enrichPathway(data$x, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2)

dotplot(result)
emapplot(result, color = "pvalue")

dataSet <- dataSets[3]

data <- read.table(dataSet, header=T)
result <- enrichPathway(data$x, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2)

dotplot(result)
emapplot(result, color = "pvalue")

dataSet <- dataSets[4]

data <- read.table(dataSet, header=T)
result <- enrichPathway(data$x, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2)

dotplot(result)
emapplot(result, color = "pvalue")

 

The loop runs without any problem, but when I go "manually" trough the datasets, the first two plots are no problem, but the next one causes an immediate crash of Rstudio (1.1.447, Win10/64bit).

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> res <- lapply(dataSets, function(dataSet) {
+ data <- read.table(dataSet, header=T)
+ enrichPathway(data$x, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2)
+ })

> emp = lapply(res, emapplot)
> cowplot::plot_grid(plotlist=emp, ncol=2)

can't reproduce any issue.

 

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Thanks for your help, I will try to implement your script.

 

Best,

Martin

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