No colors with respect to fold change and no circular plot
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- data-visualization
Research direction
Start by reproducing the provided enrichGO and cnetplot call, including foldChange, circular, and colorEdge, and inspect the reported transformation and ggrepel warnings. Trace the cnetplot entry point and determine whether fold-change colors and the circular plot are expected to work; done means the behavior is fixed or its limitation is clearly documented.
Written by the indexing model from the issue text.
Description
Hi,
I am trying to plot the results of enrichGO. Here's the code:
ego <- enrichGO(gene = sig_genes_L_O$ENTREZID,
universe = comparison_L_O$ENTREZID,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
pvalueCutoff = 0.01,
qvalueCutoff = 0.01,
readable = TRUE)
geneList <- sig_genes_L_O$Student's T-test Difference L_O
names(geneList) <- as.character(sig_genes_L_O$ENTREZID)
geneList <- geneList[!is.na(names(geneList)) & !duplicated(names(geneList))]
geneList <- sort(geneList, decreasing = TRUE)
print(cnetplot(ego,
foldChange=geneList,
categorySize="pvalue",
showCategory = 5,
circular = TRUE,
colorEdge = TRUE))
First, here are the warning I see when I try to plot the cnet plot:
Warning messages:
1: In (function (name = waiver(), ..., low = muted("red"), mid = "white", :
log-10 transformation introduced infinite values in midpoint.
2: In transformation$transform(x) : NaNs produced
3: In (function (name = waiver(), ..., low = muted("red"), mid = "white", :
log-10 transformation introduced infinite values.
4: ggrepel: 377 unlabeled data points (too many overlaps). Consider increasing max.overlaps
And, here is the plot:
Please help me with this, Thanks.
Kind regards,
Abeedha
- Dominant language
- R
- Stars
- 260
- Forks
- 75
- PR merge metrics
- No merged PRs in 30d
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