jmw86069 / multienrichjam Goto Github PK

Hello,
I am using the enrichDF2enrichResult method to convert a result data frame I obtained with webgestaltR into a enrichResult.
using the following command:

enrichResult <- enrichDF2enrichResult(
  enrichDF = df,
  pvalueCutoff = 1,
  pAdjustMethod = "FDR",
  keyColname = "geneSet",
  pathGenes = "size",
  geneColname = "userId",
  geneHits = "overlap",
  geneDelim = ";",
  pvalueColname = "pValue")

This seems to work fine and there appear no error messages. However, when I try and use the resulting Large enrichResult, e.g. with barplot or dotplot from the clusterProfiler or enrichplot package, I get the following error:

Error in ans[ypos] <- rep(yes, length.out = len)[ypos] : 
  replacement has length zero

Do you have any idea what might be the cause of this?
These are the package versions I am using:
enrichplot_1.10.1 clusterProfiler_3.18.0 multienrichjam_0.0.37.900 DOSE_3.16.0
I have also attached the table which I want to turn into the enrichResult.

enrichment_results_1610716848.txt

Cheers!

Hi,

I am getting below error while running function mem_canonical_plots

(15:52:37) 23Mar2022: mem_plot_folio(): Enrichment P-value heatmap

(15:52:37) 23Mar2022: mem_plot_folio(): plot_num 1: Enrichment P-value Heatmap

Error in ComplexHeatmap::Heatmap(use_matrix, name = name, col = col_logp, :
unused arguments (node_factor = 5, label_factor = 1.5)

Quick question:
Is it possible to disable the display of the gene name in the cnetplotJam() function? E.g. only the nodes should be annotated with the category name. The result would look similar to cnetplot(edox, node_label="category") from the enrichplot.
I looked through the internet and tried didn't settings, but I didn't manage.

Thanks!

Hello!

I'm currently trying to convert my fGSEA result data.frame into an enrichResult for further processing using the enrichplot package, however, I'm currently getting the following error in response to this input:

 >   fgsea3_1res <-enrichDF2enrichResult(
+     enrichDF = fgsea3_1,
+     pvalueCutoff = 0.05,
+     pAdjustMethod = "BH",
+     keyColname = c("pathway"),
+     pathGenes = "leadingEdge",
+     geneColname = c("leadingEdge"),
+     geneHits = "geneHits",
+     geneRatioColname = c("GeneRatio", "^Ratio"),
+     geneDelim = ",",
+     geneSep = ",",
+     pvalueColname = c("pval", "padj"),
+     descriptionColname = c("pathway"),
+     msigdbGmtT = NULL,
+     verbose = FALSE,
+     )
Error in `[.data.frame`(x, i, j, drop) : undefined columns selected

Any advice is appreciated!

Hello,

I've noticed the enrichDF2enrichResult function only works when the Term IDs are a factor and not as a character when I go to later use the cnetplot function in the enrichplot package.

When I pass a DF to enrichDF2enrichResult with Term IDs as a character and try to plot my results with cnetplot I get this error:
Error in graph.data.frame(x, directed = FALSE) : the data frame should contain at least two columns

However, it works when I pass the same DF to enrichDF2enrichResult with Term IDs as a factor and then use cnetplot

I have clusterProfiler v3.16.0 and multienrichjam v0.0.35.900 installed

Wondering if you had any thoughts

I have included a reproducible example below:

#Create Term IDs as character
Term.ID <- c("GO:0001501", "GO:0001503", "GO:0001525", "GO:0001568", "GO:0001775", "GO:0001816", "GO:0001817", "GO:0001944", "GO:0001952", "GO:0002376")
#Also create Term IDs as factor
Term.ID.factor <- factor(Term.ID)
#List enriched genes of each Term ID
Genes <- c("COL3A1/COL5A2/FGFR1/JAG2/LUM/MSX1/POH/STC1/TIMP1/VCAN", "COL5A2/JAG1/POH/PTK2/SPP1/STC1/VCAN", "FGFR1/ITGAV/JAG1/NRP1/PDGFA/PF4/PTK2/VAV2/VEGFA", "COL3A1/FGFR1/ITGAV/JAG1/NRP1/PDGFA/PTK2/VAV2/VEGFA", "APP/COL3A1/CXCL6/ITGAV/JAG2/OLR1/PDGFA/PF4/PGLYRP1/POH/PRG2/THBD/TIMP1/TNFRSF21/VAV2", "APP/CXCL6/FGFR1/ITGAV/LPL/LUM/PF4/PGLYRP1/POSTN/TNFRSF21", "APP/CXCL6/FGFR1/ITGAV/LPL/LUM/PF4/PGLYRP1/POSTN/TNFRSF21", "COL3A1/FGFR1/ITGAV/JAG1/NRP1/PDGFA/PF4/PTK2/VAV2/VEGFA", "JAG1/NRP1/POSTN/PTK2/VEGFA", "APP/COL3A1/CXCL6/ITGAV/JAG1/JAG2/OLR1/PF4/PGLYRP1/POH/PRG2/PTK2/THBD/TNFRSF21/VAV2/VEGFA/VTN")
E.value <- c(1.25e-05, 2.01e-02, 1.11e-03, 1.34e-03, 1.24e-06, 1.11e-03, 4.53e-04, 1.02e-03, 1.62e-02, 1.25e-03)
#Term ID Description
Description <- c("skeletal system development", "ossification", "angiogenesis", "blood vessel development", "cell activation", "cytokine production", "regulation of cytokine production", "vasculature development", "regulation of cell-matrix adhesion", "immune system process")
#Create DFs
test_df <- cbind.data.frame(Term.ID, Genes, E.value, Description)
test_df_factor <- cbind.data.frame(Term.ID.factor, Genes, E.value, Description)
colnames(test_df_factor) <- c("Term.ID", "Genes", "E.value", "Description")

ego <- enrichDF2enrichResult(test_df, keyColname = "Term.ID", geneColname = "Genes", pvalueColname = "E.value", pvalueCutoff=0.05, pAdjustMethod="none", verbose = TRUE)
ego_factor <- enrichDF2enrichResult(test_df_factor, keyColname = "Term.ID", geneColname = "Genes", pvalueColname = "E.value", pvalueCutoff=0.05, pAdjustMethod="none", verbose = TRUE)

#Has error
cnetplot(ego)

#Works
cnetplot(ego_factor)

Hello,

I ran into an issue with multiEnrichMap, where it would sometimes fail with "undefined columns selected" error. In the browser mode I found out that the function is attempting to remove duplicates during name vector creation, but subsetting with a character vector containing NAs. After some digging around I found out that is because of line 603 in jamenrich-base.r the require_non_na is set to FALSE:

directionColname <- find_colname(directionColname,
     iDF1,
     require_non_na=FALSE);

Is this by design? When I changed the variable to TRUE it fixed my problem. Are there any potential problems I might run into by changing this behavior?

Hello

I am very interesting in the function enrichDF2enrichResult but I could not install your package.

At the begining, the package nmormt was the issue because it is not available for 3.6 R version.
I downloaded the new version of R (4.0) but the problem is now with jamba which is not available on R 4.0 at the time. How can I do?

Morover, I wanted more information about the input for that function. Which results from GSEA enrichment are require?

Thank you

Emilie

Hi, I tried converting S4 object to the data frame and then tried reconverting it to the S4 class using "multienrichjam" package. I found the following error. Any help would be really appreciated.

library(DOSE)
data(geneList)
de <- names(geneList)[abs(geneList) > 2]

edo <- enrichDGN(de)
edo_df<-as.data.frame(edo)

library(multienrichjam)
test<-enrichDF2enrichResult(edo_df)

output: Error in renameColumn(enrichDF, from = c(keyColname, pvalueColname, geneColname), : could not find function "renameColumn"