enrichplot
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YuLab-SMU
ridgeplot showCategory doesn't accept vector of specific pathways
library(clusterProfiler)
library(msigdbr)
data(geneList, package="DOSE")
C3_t2g <- msigdbr(species = "Homo sapiens", category = "C3") %>%
dplyr::select(gs_name, entrez_gene)
em2 <- GSEA(geneList, TERM2GENE = C3_t2g)
set.seed(2020-10-27)
selected_pathways <- sample(em2$Description, 10)
ridgeplot(em2, showCategory = selected_pathways)
Error in seq_len(n) : argument must be coercible to non-negative integer
In addition: Warning messages:
1: In seq_len(n) : first element used of 'length.out' argument
2: In ridgeplot.gseaResult(x, showCategory = showCategory, fill = fill, :
NAs introduced by coercion
https://github.com/YuLab-SMU/enrichplot/blob/master/R/ridgeplot.R#L41-L46
I kindly would like support this feature request, also because of this thread at the Bioconductor support pages: https://support.bioconductor.org/p/9146375/
Thanks for adding support for this, but unfortunately it doesn't work yet....
> library(clusterProfiler)
> library(org.Hs.eg.db)
> library(enrichplot)
> library(ggplot2)
>
> data(geneList, package="DOSE")
>
> set.seed(22) # for reproducibility
>
> # generate some results
> ego <- gseGO(geneList = geneList,
+ OrgDb = org.Hs.eg.db,
+ ont = "BP",
+ minGSSize = 100,
+ maxGSSize = 500,
+ eps = 0,
+ pAdjustMethod = "BH",
+ pvalueCutoff = 0.05,
+ verbose = FALSE)
> # show only 4 randomly selected gene sets.
> GOcats4vis <- data.frame(ego)$Description[ sample(1:dim(data.frame(ego))[1], size = 4) ]
> GOcats4vis
[1] "cardiac chamber development" "renal system process"
[3] "kidney epithelium development" "regulation of Wnt signaling pathway"
>
> ## plotting these gene sets in a ridgeplot doesn't work yet...
> ridgeplot(ego, showCategory=GOcats4vis, orderBy = "setSize")
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] :
replacement has length zero
In addition: Warning message:
In rep(yes, length.out = len) : 'x' is NULL so the result will be NULL
>
> ## ... but still does if provided a number.
> ridgeplot(ego, showCategory=8, orderBy = "setSize")
Picking joint bandwidth of 0.281
>
> ## in contrast, dotplot works when specifying gene sets.
> dotplot(ego, showCategory=GOcats4vis, orderBy = "setSize")
>
> packageVersion("enrichplot")
[1] ‘1.23.1’
>
>
>
> ridgeplot(ego, showCategory=GOcats4vis, orderBy = "setSize")
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] :
replacement has length zero
In addition: Warning message:
In rep(yes, length.out = len) : 'x' is NULL so the result will be NULL
> traceback()
17: ifelse(is.na(coord_limits), limits, coord_limits)
16: expand_limits_continuous_trans(range_continuous, expand, coord_limits,
trans)
15: expand_limits_discrete_trans(limits, expand, coord_limits, range_continuous = range_continuous)
14: expand_limits_discrete(limits, expand, coord_limits, range_continuous = scale$range_c$range)
13: expand_limits_scale(scale, expansion, limits, coord_limits = coord_limits)
12: view_scales_from_scale(scale_y, self$limits$y, self$expand)
11: setup_panel_params(..., self = self)
10: self$coord$setup_panel_params(scale_x, scale_y, params = self$coord_params)
9: (function (scale_x, scale_y)
{
self$coord$setup_panel_params(scale_x, scale_y, params = self$coord_params)
})(dots[[1L]][[1L]], dots[[2L]][[1L]])
8: mapply(FUN = f, ..., SIMPLIFY = FALSE)
7: Map(setup_panel_params, scales_x, scales_y)
6: setup_panel_params(..., self = self)
5: layout$setup_panel_params()
4: ggplot_build.ggplot(x)
3: ggplot_build(x)
2: print.ggplot(x)
1: (function (x, ...)
UseMethod("print"))(x)
>
Again thanks for adding support for this, but it unfortunately it is no longer working
> library(clusterProfiler)
> library(org.Hs.eg.db)
> library(enrichplot)
> library(ggplot2)
> data(geneList, package="DOSE")
> set.seed(22) # for reproducibility
> # generate some results
> ego <- gseGO(geneList = geneList,
+ OrgDb = org.Hs.eg.db,
+ ont = "BP",
+ minGSSize = 100,
+ maxGSSize = 500,
+ eps = 0,
+ pAdjustMethod = "BH",
+ pvalueCutoff = 0.05,
+ verbose = FALSE)
> # show only 4 randomly selected gene sets.
> GOcats4vis <- data.frame(ego)$Description[ sample(1:dim(data.frame(ego))[1], size = 4) ]
> GOcats4vis
[1] "cardiac chamber development" "renal system process" "kidney epithelium development"
[4] "regulation of Wnt signaling pathway"
> ## plotting these gene sets in a ridgeplot doesn't work yet...
> ridgeplot(ego, showCategory=GOcats4vis, orderBy = "setSize")
Error in seq_len(n) : argument must be coercible to non-negative integer
In addition: Warning messages:
1: In seq_len(n) : first element used of 'length.out' argument
2: In ridgeplot.gseaResult(x, showCategory = showCategory, fill = fill, :
NAs introduced by coercion
> traceback()
3: ridgeplot.gseaResult(x, showCategory = showCategory, fill = fill,
core_enrichment = core_enrichment, label_format = label_format,
...)
2: ridgeplot(ego, showCategory = GOcats4vis, orderBy = "setSize")
1: ridgeplot(ego, showCategory = GOcats4vis, orderBy = "setSize")
> ## ... but still does if provided a number.
> ridgeplot(ego, showCategory=8, orderBy = "setSize")
Picking joint bandwidth of 0.281
> ## in contrast, dotplot works when specifying gene sets.
> dotplot(ego, showCategory=GOcats4vis, orderBy = "setSize")
> packageVersion("enrichplot")
[1] ‘1.22.0’
> session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.2 (2023-10-31)
os macOS Ventura 13.5.2
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2024-02-13
rstudio 2023.06.0+421 Mountain Hydrangea (desktop)
pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
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EnhancedVolcano * 1.13.2 2024-02-05 [1] Github (benjibromberg/EnhancedVolcano@6d1a0f6)
enrichplot * 1.22.0 2023-11-06 [1] Bioconductor
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GO.db 3.18.0 2023-12-12 [1] Bioconductor
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[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
You will have to update enrichplot; note that the fix is not available in v1.22 (= release version) that you are using.
> BiocManager::install(c('YuLab-SMU/enrichplot'), force=TRUE)
>
> packageVersion("enrichplot")
[1] ‘1.23.1.992’
>
After running your code I then get:
Oh thanks @guidohooiveld!!
I totally didn't realize it was only available through the git release so far! Much appreciated!!!