mj-kamal
commented
2 days ago Solved the issue, problem was the layout argument, this has been updated to use igraph layouts. Leaving this up in case anyone else has the same problem.
Open mj-kamal opened 2 days ago
mj-kamal
commented
2 days ago Solved the issue, problem was the layout argument, this has been updated to use igraph layouts. Leaving this up in case anyone else has the same problem.
mj-kamal
commented
1 day ago emapplot won't display legend for adjusted p values.
Code:
DE_go_BP <- enrichGO(gene = allDE_target_entr, OrgDb = org.Mm.eg.db, keyType = "ENTREZID", ont = "BP") DE_go_BP_PT <- pairwise_termsim(DE_go_BP)
emapplot(DE_go_BP_PT,
group = TRUE,
showCategory = 50,
size_category = 0.5,
layout = igraph::layout_with_kk,
node_label = "none",
color = "p.adjust")
I get the following error:
Warning messages:
1: `guide_colourbar()` cannot be used for colour_ggnewscale_1.
ℹ Use one of colour, color, or fill instead.
2: `guide_colourbar()` needs continuous scales. 
guidohooiveld
commented
1 day ago FWIW: the warning AND disappearance of the color legend for (adjusted) pvalues are caused because of the argument group=TRUE. If it is set to group=FALSE (which is default), there is no warning and the color legend is plotted.
@GuangchuangYu : could you please have a look at this?
Reproducible example:
> library(clusterProfiler)
> library(org.Hs.eg.db)
> library(enrichplot)
> library(ggplot2)
>
> ## load and prepare example data / results
> data(geneList, package="DOSE")
>
> up <- names(geneList)[abs(geneList) > 2]
>
> ## run ORA using GOBP categories
> res.up <- enrichGO(gene = up,
+ OrgDb = org.Hs.eg.db,
+ ont = "BP",
+ pAdjustMethod = "BH",
+ pvalueCutoff = 0.01,
+ qvalueCutoff = 0.05,
+ readable = TRUE)
>
> res.up <- pairwise_termsim(res.up)
> head(res.up)
ID Description GeneRatio BgRatio
GO:0098813 GO:0098813 nuclear chromosome segregation 34/196 324/18986
GO:0000819 GO:0000819 sister chromatid segregation 30/196 235/18986
GO:0140014 GO:0140014 mitotic nuclear division 32/196 282/18986
GO:0000070 GO:0000070 mitotic sister chromatid segregation 28/196 194/18986
GO:0007059 GO:0007059 chromosome segregation 37/196 429/18986
GO:0000280 GO:0000280 nuclear division 37/196 451/18986
RichFactor FoldEnrichment zScore pvalue p.adjust
GO:0098813 0.10493827 10.165092 16.99418 1.637859e-24 2.862638e-21
GO:0000819 0.12765957 12.366044 17.90610 3.280746e-24 2.862638e-21
GO:0140014 0.11347518 10.992039 17.26559 3.668997e-24 2.862638e-21
GO:0000070 0.14432990 13.980854 18.56041 3.796601e-24 2.862638e-21
GO:0007059 0.08624709 8.354526 15.73618 1.283918e-23 7.744593e-21
GO:0000280 0.08203991 7.946989 15.24960 7.364511e-23 3.701894e-20
qvalue
GO:0098813 2.487773e-21
GO:0000819 2.487773e-21
GO:0140014 2.487773e-21
GO:0000070 2.487773e-21
GO:0007059 6.730433e-21
GO:0000280 3.217129e-20
geneID
GO:0098813 CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/TACC3/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/PTTG1
GO:0000819 CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/TOP2A/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/TACC3/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/CCNB1/KIF4A
GO:0140014 CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/UBE2S/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/CHEK1/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/BMP4
GO:0000070 CDCA8/CDC20/KIF23/CENPE/MYBL2/NDC80/NCAPH/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/CCNB1/KIF4A
GO:0007059 CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/HJURP/SKA1/NUSAP1/TPX2/TACC3/NEK2/CENPM/CENPN/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/PTTG1
GO:0000280 CDCA8/CDC20/KIF23/CENPE/MYBL2/CCNB2/NDC80/TOP2A/NCAPH/ASPM/DLGAP5/UBE2C/SKA1/NUSAP1/TPX2/NEK2/RAD51AP1/UBE2S/CDK1/MAD2L1/KIF18A/CDT1/BIRC5/KIF11/TTK/NCAPG/AURKB/CHEK1/TRIP13/PRC1/KIFC1/KIF18B/AURKA/CCNB1/KIF4A/PTTG1/BMP4
Count
GO:0098813 34
GO:0000819 30
GO:0140014 32
GO:0000070 28
GO:0007059 37
GO:0000280 37
>
> ## make emapplot
> ## using default settings,
> ## NO warning + color legend p.adjust is plotted
> emapplot(res.up)
> > ## WARNING and NO color legend; when group = TRUE
> emapplot(res.up, group = TRUE)
Warning messages:
1: `guide_colourbar()` cannot be used for colour_ggnewscale_1.
ℹ Use one of colour, color, or fill instead.
2: `guide_colourbar()` needs continuous scales.
>
> sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Europe/Amsterdam
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_3.5.1 igraph_2.1.1 enrichplot_1.27.1.004
[4] org.Hs.eg.db_3.20.0 AnnotationDbi_1.68.0 IRanges_2.40.0
[7] S4Vectors_0.44.0 Biobase_2.66.0 BiocGenerics_0.52.0
[10] clusterProfiler_4.14.3
loaded via a namespace (and not attached):
[1] DBI_1.2.3 gson_0.1.0 remotes_2.5.0
[4] rlang_1.1.4 magrittr_2.0.3 DOSE_4.0.0
[7] compiler_4.4.2 RSQLite_2.3.7 systemfonts_1.1.0
[10] png_0.1-8 callr_3.7.6 vctrs_0.6.5
[13] reshape2_1.4.4 stringr_1.5.1 pkgconfig_2.0.3
[16] crayon_1.5.3 fastmap_1.2.0 XVector_0.46.0
[19] labeling_0.4.3 utf8_1.2.4 UCSC.utils_1.2.0
[22] ps_1.8.1 purrr_1.0.2 bit_4.5.0
[25] zlibbioc_1.52.0 cachem_1.1.0 aplot_0.2.3
[28] GenomeInfoDb_1.42.0 jsonlite_1.8.9 blob_1.2.4
[31] tweenr_2.0.3 BiocParallel_1.40.0 parallel_4.4.2
[34] R6_2.5.1 stringi_1.8.4 RColorBrewer_1.1-3
[37] GOSemSim_2.32.0 Rcpp_1.0.13-1 snow_0.4-4
[40] ggtangle_0.0.4.004 R.utils_2.12.3 Matrix_1.7-1
[43] splines_4.4.2 tidyselect_1.2.1 qvalue_2.38.0
[46] codetools_0.2-20 curl_6.0.1 processx_3.8.4
[49] pkgbuild_1.4.5 lattice_0.22-6 tibble_3.2.1
[52] plyr_1.8.9 treeio_1.30.0 withr_3.0.2
[55] KEGGREST_1.46.0 gridGraphics_0.5-1 desc_1.4.3
[58] polyclip_1.10-7 Biostrings_2.74.0 pillar_1.9.0
[61] BiocManager_1.30.25 ggtree_3.14.0 ggfun_0.1.7
[64] generics_0.1.3 munsell_0.5.1 scales_1.3.0
[67] tidytree_0.4.6 glue_1.8.0 lazyeval_0.2.2
[70] tools_4.4.2 ggnewscale_0.5.0 data.table_1.16.2
[73] fgsea_1.32.0 fs_1.6.5 fastmatch_1.1-4
[76] cowplot_1.1.3 grid_4.4.2 tidyr_1.3.1
[79] ape_5.8 colorspace_2.1-1 nlme_3.1-166
[82] GenomeInfoDbData_1.2.13 patchwork_1.3.0 ggforce_0.4.2
[85] cli_3.6.3 fansi_1.0.6 dplyr_1.1.4
[88] gtable_0.3.6 R.methodsS3_1.8.2 yulab.utils_0.1.8
[91] digest_0.6.37 ggrepel_0.9.6 ggplotify_0.1.2
[94] farver_2.1.2 memoise_2.0.1 R.oo_1.27.0
[97] lifecycle_1.0.4 httr_1.4.7 GO.db_3.20.0
[100] bit64_4.5.2 MASS_7.3-61
>Yes, you are correct. It must be a problem with one of the recent enrichplot versions. The last time I ran it, it was with V1.20.3 and group = TRUE didn't give this error and I was still able to cluster the nodes and colour them with p.adjust/display the legend.
It's also worth noting that in the current version of enrichplot (V1.26.2), using the group = TRUE argument will still colour the nodes according to some metric, even if the color = "p.adjust" argument is missing from the function. Interestingly, the plots generated look identifical whether or not you include color = "p.adjust"
Hopefully there is an easy fix for this because I need to cluster the terms and plot the p.adjust as colors. It would also be good to have a way to set color = "black" or something in case you didn't want to plot the p-value or you wanted the size to correspond to the p-values and the colours to correspond to the size.
Hello,
I've gotten a new error that I didn't get with a previous version of R & enrichplot
My code:
DE_go_BP <- enrichGO(gene = allDE_target_entr, OrgDb = org.Mm.eg.db, keyType = "ENTREZID", ont = "BP") DE_go_BP_PT <- pairwise_termsim(DE_go_BP) emapplot(DE_go_BP_PT, showCategory = 50, layout = "nicely", group )Got this error:
Error in storage.mode(mat) <- "integer" : 'list' object cannot be coerced to type 'integer'R version 4.4.2 (2024-10-31) clusterProfiler V 4.14.3 enrichplot V1.26.2