clusterProfiler
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dotplot: wrong orderBy parameter; set to default `orderBy = "x"`
The plot is created, but I have no idea on the error. I have a DEG set produced by DeSeq2. I get the sorted ranked with ENSEMBL names (hg38) as:
head(geneListDF)
ENSG00000256377 ENSG00000159713 ENSG00000176387 ENSG00000113296 ENSG00000174059
8.132732 6.644455 5.898174 5.744217 5.668175
ENSG00000130592
5.475563
I generate the enriched list:
ego3 <- gseGO(geneList = geneListDF,
OrgDb = org.Hs.eg.db,
ont = "BP",
keyType = "ENSEMBL",
minGSSize = 100,
maxGSSize = 500,
pvalueCutoff = 0.05,
verbose = FALSE)
then I try to produce the plot:
dotplot(ego3, showCategory=20)
wrong orderBy parameter; set to default `orderBy = "x"`
The plot is actually created, but I am wondered why this error.
ego3
#
# Gene Set Enrichment Analysis
#
#...@organism Homo sapiens
#...@setType BP
#...@keytype ENSEMBL
#...@geneList Named num [1:32522] 8.13 6.64 5.9 5.74 5.67 ...
- attr(*, "names")= chr [1:32522] "ENSG00000256377" "ENSG00000159713" "ENSG00000176387" "ENSG00000113296" ...
#...nPerm
#...pvalues adjusted by 'BH' with cutoff <0.05
#...831 enriched terms found
'data.frame': 831 obs. of 11 variables:
$ ID : chr "GO:0000070" "GO:0000082" "GO:0000280" "GO:0000819" ...
$ Description : chr "mitotic sister chromatid segregation" "G1/S transition of mitotic cell cycle" "nuclear division" "sister chromatid segregation" ...
$ setSize : int 160 254 408 188 194 270 154 183 317 157 ...
$ enrichmentScore: num -0.623 -0.474 -0.53 -0.612 -0.531 ...
$ NES : num -2.6 -2.11 -2.48 -2.61 -2.28 ...
$ pvalue : num 1e-10 1e-10 1e-10 1e-10 1e-10 ...
$ p.adjust : num 3.24e-09 3.24e-09 3.24e-09 3.24e-09 3.24e-09 ...
$ qvalues : num 1.15e-09 1.15e-09 1.15e-09 1.15e-09 1.15e-09 ...
$ rank : num 5522 6746 5530 5857 5254 ...
$ leading_edge : chr "tags=43%, list=17%, signal=36%" "tags=37%, list=21%, signal=29%" "tags=36%, list=17%, signal=30%" "tags=43%, list=18%, signal=35%" ...
$ core_enrichment: chr "ENSG00000085415/ENSG00000121579/ENSG00000108424/ENSG00000198887/ENSG00000149636/ENSG00000168802/ENSG00000132341"| __truncated__ "ENSG00000131023/ENSG00000149308/ENSG00000162676/ENSG00000169016/ENSG00000156273/ENSG00000253729/ENSG00000150457"| __truncated__ "ENSG00000154429/ENSG00000085415/ENSG00000121579/ENSG00000139351/ENSG00000134278/ENSG00000108424/ENSG00000105173"| __truncated__ "ENSG00000197771/ENSG00000198824/ENSG00000062650/ENSG00000116560/ENSG00000085415/ENSG00000121579/ENSG00000108424"| __truncated__ ...
#...Citation
Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
clusterProfiler: an R package for comparing biological themes among
gene clusters. OMICS: A Journal of Integrative Biology
2012, 16(5):284-287
Any ideas?
My session:
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] enrichplot_1.10.2 manhattanly_0.3.0
[3] heatmaply_1.3.0 viridis_0.6.2
[5] viridisLite_0.4.0 plotly_4.10.0
[7] writexl_1.4.0 pathview_1.30.1
[9] biomaRt_2.46.3 AnnotationHub_2.22.1
[11] BiocFileCache_1.14.0 dbplyr_2.1.1
[13] org.Hs.eg.db_3.12.0 AnnotationDbi_1.52.0
[15] plyr_1.8.6 clusterProfiler_3.18.1
[17] ggrepel_0.9.1 ggplot2_3.3.5
[19] pheatmap_1.0.12 RColorBrewer_1.1-2
[21] DESeq2_1.30.1 SummarizedExperiment_1.20.0
[23] Biobase_2.50.0 MatrixGenerics_1.2.1
[25] matrixStats_0.61.0 GenomicRanges_1.42.0
[27] GenomeInfoDb_1.26.7 IRanges_2.24.1
[29] S4Vectors_0.28.1 BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] snow_0.4-4 shadowtext_0.1.1
[3] fastmatch_1.1-3 igraph_1.2.11
[5] lazyeval_0.2.2 splines_4.0.3
[7] crosstalk_1.2.0 BiocParallel_1.24.1
[9] digest_0.6.29 foreach_1.5.2
[11] yulab.utils_0.0.4 htmltools_0.5.2
[13] GOSemSim_2.16.1 GO.db_3.12.1
[15] fansi_1.0.2 magrittr_2.0.2
[17] memoise_2.0.1 tzdb_0.2.0
[19] Biostrings_2.58.0 annotate_1.68.0
[21] graphlayouts_0.8.0 vroom_1.5.7
[23] askpass_1.1 prettyunits_1.1.1
[25] colorspace_2.0-2 blob_1.2.2
[27] rappdirs_0.3.3 xfun_0.29
[29] dplyr_1.0.8 crayon_1.5.0
[31] RCurl_1.98-1.6 jsonlite_1.7.3
[33] graph_1.68.0 scatterpie_0.1.7
[35] genefilter_1.72.1 iterators_1.0.14
[37] survival_3.2-7 glue_1.6.1
[39] polyclip_1.10-0 registry_0.5-1
[41] gtable_0.3.0 zlibbioc_1.36.0
[43] XVector_0.30.0 webshot_0.5.2
[45] DelayedArray_0.16.3 Rgraphviz_2.34.0
[47] scales_1.1.1 DOSE_3.16.0
[49] DBI_1.1.2 Rcpp_1.0.8
[51] xtable_1.8-4 progress_1.2.2
[53] bit_4.0.4 htmlwidgets_1.5.4
[55] httr_1.4.2 fgsea_1.16.0
[57] ellipsis_0.3.2 pkgconfig_2.0.3
[59] XML_3.99-0.8 farver_2.1.0
[61] locfit_1.5-9.4 utf8_1.2.2
[63] tidyselect_1.1.1 labeling_0.4.2
[65] rlang_1.0.1 reshape2_1.4.4
[67] later_1.3.0 munsell_0.5.0
[69] BiocVersion_3.12.0 tools_4.0.3
[71] cachem_1.0.6 downloader_0.4
[73] cli_3.2.0 generics_0.1.2
[75] RSQLite_2.2.10 stringr_1.4.0
[77] fastmap_1.1.0 yaml_2.3.4
[79] bit64_4.0.5 tidygraph_1.2.0
[81] purrr_0.3.4 dendextend_1.15.2
[83] KEGGREST_1.30.1 ggraph_2.0.5
[85] mime_0.12 KEGGgraph_1.50.0
[87] DO.db_2.9 xml2_1.3.3
[89] compiler_4.0.3 rstudioapi_0.13
[91] png_0.1-7 curl_4.3.2
[93] interactiveDisplayBase_1.28.0 tibble_3.1.6
[95] tweenr_1.0.2 geneplotter_1.68.0
[97] stringi_1.7.6 lattice_0.20-41
[99] Matrix_1.4-0 vctrs_0.3.8
[101] pillar_1.7.0 lifecycle_1.0.1
[103] BiocManager_1.30.16 data.table_1.14.2
[105] cowplot_1.1.1 bitops_1.0-7
[107] seriation_1.3.2 httpuv_1.6.5
[109] qvalue_2.22.0 R6_2.5.1
[111] TSP_1.1-11 promises_1.2.0.1
[113] gridExtra_2.3 codetools_0.2-16
[115] MASS_7.3-53 assertthat_0.2.1
[117] openssl_1.4.6 withr_2.4.3
[119] GenomeInfoDbData_1.2.4 hms_1.1.1
[121] grid_4.0.3 ggfun_0.0.5
[123] tidyr_1.2.0 rvcheck_0.2.1
[125] ggforce_0.3.3 shiny_1.7.1
[127] tinytex_0.37
This had been fixed by the release version of enrichplot
.
I am a bit confused. How do I update to the latest version? Am I using the:
library(remotes)
install_github(c("GuangchuangYu/DOSE", "GuangchuangYu/clusterProfiler", "GuangchuangYu/enrichplot" ))
or something else?this might be relevant #434 Thank you!