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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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Error in enrichplot for class "compareClusterResult" in gseGO #430

Open BhardwajArch opened 2 years ago

BhardwajArch commented 2 years ago

I am using updated version of clusterProfiler. I have geneList from multiple groups and interested in doing "gseGO" and "gseKEGG" analysis . I prepared input and got significant GO terms.

_resout <- compareCluster(listInput, fun="gseGO",OrgDb = org.Hs.eg.db)

Next checked the class of output variable and enriched GO terms :

class(res_out) [1] "compareClusterResult" attr(,"package") [1] "DOSE"

head(res_out) Cluster ID Description setSize 1 BL_vsAML.txt GO:0002377 immunoglobulin production 68 2 BL_vsAML.txt GO:0050853 B cell receptor signaling pathway 51 3 BL_vsAML.txt GO:0050871 positive regulation of B cell activation 53 4 BL_vsAML.txt GO:0016064 immunoglobulin mediated immune response 68 5 BL_vsAML.txt GO:0019724 B cell mediated immunity 69 6 BL_vsAML.txt GO:0050851 antigen receptor-mediated signaling pathway 84 enrichmentScore NES pvalue p.adjust qvalues rank 1 0.7536202 2.867325 1e-10 5.838333e-08 5.352632e-08 827 2 0.7723045 2.745827 1e-10 5.838333e-08 5.352632e-08 581 3 0.7179211 2.578551 1e-10 5.838333e-08 5.352632e-08 749 4 0.6684648 2.543331 1e-10 5.838333e-08 5.352632e-08 842 5 0.6628316 2.530057 1e-10 5.838333e-08 5.352632e-08 842 6 0.6173177 2.479274 1e-10 5.838333e-08 5.352632e-08 581

As a result, I tried to get enrichplot to display cluster based results ##### _result.out <- enrichplot::pairwise_termsim(resout)

But it gives me error :

result.out <- enrichplot::pairwise_termsim(res_out) Error in $<-.data.frame(*tmp*, "Cluster", value = NAinteger) : replacement has 1 row, data has 0

I would appreciate all the suggestions

huerqiang commented 2 years ago

@BhardwajArch Please also install the Github version of enrichplot and DOSE. If the the error still exists, please send the input data to my email: "13766876214@163.com".

huerqiang commented 2 years ago

@BhardwajArch Your data work well with the Github version of clusterProfiler, enrichplot and DOSE. Please check your package version. This is my sessioninfo:

> devtools::session_info()
- Session info  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 hash: backhand index pointing right: medium skin tone, waving hand: dark skin tone, scarf

 setting  value
 version  R version 4.1.1 (2021-08-10)
 os       Windows 10 x64 (build 18363)
 system   x86_64, mingw32
 ui       Rgui
 language (EN)
 collate  Chinese (Simplified)_China.936
 ctype    Chinese (Simplified)_China.936
 tz       Asia/Taipei
 date     2022-02-09
 pandoc   2.10.1 @ C:\\Users\\Dell\\AppData\\Local\\Pandoc\\pandoc.exe

- Packages -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 package          * version    date (UTC) lib source
 AnnotationDbi    * 1.56.2     2021-11-09 [1] Bioconductor
 ape                5.5        2021-04-25 [1] CRAN (R 4.1.1)
 aplot              0.1.1      2021-09-22 [1] CRAN (R 4.1.1)
 assertthat         0.2.1      2019-03-21 [1] CRAN (R 4.1.1)
 Biobase          * 2.54.0     2021-10-26 [1] Bioconductor
 BiocGenerics     * 0.40.0     2021-10-26 [1] Bioconductor
 BiocParallel       1.28.0     2021-10-26 [1] Bioconductor
 Biostrings         2.62.0     2021-10-26 [1] Bioconductor
 bit                4.0.4      2020-08-04 [1] CRAN (R 4.1.1)
 bit64              4.0.5      2020-08-30 [1] CRAN (R 4.1.1)
 bitops             1.0-7      2021-04-24 [1] CRAN (R 4.1.1)
 blob               1.2.2      2021-07-23 [1] CRAN (R 4.1.1)
 cachem             1.0.6      2021-08-19 [1] CRAN (R 4.1.1)
 callr              3.7.0      2021-04-20 [1] CRAN (R 4.1.1)
 cli                3.1.0      2021-10-27 [1] CRAN (R 4.1.1)
 clusterProfiler  * 4.3.2.991  2022-01-27 [1] Bioconductor
 colorspace         2.0-2      2021-06-24 [1] CRAN (R 4.1.1)
 crayon             1.4.2      2021-10-29 [1] CRAN (R 4.1.1)
 data.table         1.14.2     2021-09-27 [1] CRAN (R 4.1.1)
 DBI                1.1.1      2021-01-15 [1] CRAN (R 4.1.1)
 desc               1.4.0      2021-09-28 [1] CRAN (R 4.1.1)
 devtools           2.4.2      2021-06-07 [1] CRAN (R 4.1.1)
 digest             0.6.28     2021-09-23 [1] CRAN (R 4.1.1)
 DO.db              2.9        2021-11-13 [1] Bioconductor
 DOSE               3.21.2     2022-01-27 [1] Bioconductor
 downloader         0.4        2015-07-09 [1] CRAN (R 4.1.1)
 dplyr              1.0.7      2021-06-18 [1] CRAN (R 4.1.1)
 ellipsis           0.3.2      2021-04-29 [1] CRAN (R 4.1.1)
 enrichplot         1.15.2.900 2022-01-27 [1] Bioconductor
 fansi              0.5.0      2021-05-25 [1] CRAN (R 4.1.1)
 farver             2.1.0      2021-02-28 [1] CRAN (R 4.1.1)
 fastmap            1.1.0      2021-01-25 [1] CRAN (R 4.1.1)
 fastmatch          1.1-3      2021-07-23 [1] CRAN (R 4.1.1)
 fgsea              1.20.0     2021-10-26 [1] Bioconductor
 fs                 1.5.0      2020-07-31 [1] CRAN (R 4.1.1)
 generics           0.1.1      2021-10-25 [1] CRAN (R 4.1.1)
 GenomeInfoDb       1.30.0     2021-10-26 [1] Bioconductor
 GenomeInfoDbData   1.2.7      2021-11-13 [1] Bioconductor
 ggforce            0.3.3      2021-03-05 [1] CRAN (R 4.1.1)
 ggfun              0.0.5      2022-01-20 [1] CRAN (R 4.1.2)
 ggplot2            3.3.5      2021-06-25 [1] CRAN (R 4.1.1)
 ggplotify          0.1.0      2021-09-02 [1] CRAN (R 4.1.1)
 ggraph             2.0.5      2021-02-23 [1] CRAN (R 4.1.1)
 ggrepel            0.9.1      2021-01-15 [1] CRAN (R 4.1.1)
 ggtree             3.2.0      2021-10-26 [1] Bioconductor
 glue               1.5.0      2021-11-07 [1] CRAN (R 4.1.1)
 GO.db              3.14.0     2021-11-13 [1] Bioconductor
 GOSemSim           2.20.0     2021-10-26 [1] Bioconductor
 graphlayouts       0.7.2      2021-11-21 [1] CRAN (R 4.1.2)
 gridExtra          2.3        2017-09-09 [1] CRAN (R 4.1.1)
 gridGraphics       0.5-1      2020-12-13 [1] CRAN (R 4.1.1)
 gtable             0.3.0      2019-03-25 [1] CRAN (R 4.1.1)
 httr               1.4.2      2020-07-20 [1] CRAN (R 4.1.1)
 igraph             1.2.7      2021-10-15 [1] CRAN (R 4.1.1)
 IRanges          * 2.28.0     2021-10-26 [1] Bioconductor
 jsonlite           1.7.2      2020-12-09 [1] CRAN (R 4.1.1)
 KEGGREST           1.34.0     2021-10-26 [1] Bioconductor
 lattice            0.20-45    2021-09-22 [1] CRAN (R 4.1.1)
 lazyeval           0.2.2      2019-03-15 [1] CRAN (R 4.1.1)
 lifecycle          1.0.1      2021-09-24 [1] CRAN (R 4.1.1)
 magrittr           2.0.1      2020-11-17 [1] CRAN (R 4.1.1)
 MASS               7.3-54     2021-05-03 [1] CRAN (R 4.1.1)
 Matrix             1.3-4      2021-06-01 [1] CRAN (R 4.1.1)
 memoise            2.0.0      2021-01-26 [1] CRAN (R 4.1.1)
 munsell            0.5.0      2018-06-12 [1] CRAN (R 4.1.1)
 nlme               3.1-153    2021-09-07 [1] CRAN (R 4.1.1)
 org.Hs.eg.db     * 3.14.0     2021-11-14 [1] Bioconductor
 patchwork          1.1.1      2020-12-17 [1] CRAN (R 4.1.1)
 pillar             1.6.4      2021-10-18 [1] CRAN (R 4.1.1)
 pkgbuild           1.2.0      2020-12-15 [1] CRAN (R 4.1.1)
 pkgconfig          2.0.3      2019-09-22 [1] CRAN (R 4.1.1)
 pkgload            1.2.3      2021-10-13 [1] CRAN (R 4.1.1)
 plyr               1.8.6      2020-03-03 [1] CRAN (R 4.1.1)
 png                0.1-7      2013-12-03 [1] CRAN (R 4.1.1)
 polyclip           1.10-0     2019-03-14 [1] CRAN (R 4.1.1)
 prettyunits        1.1.1      2020-01-24 [1] CRAN (R 4.1.1)
 processx           3.5.2      2021-04-30 [1] CRAN (R 4.1.1)
 ps                 1.6.0      2021-02-28 [1] CRAN (R 4.1.1)
 purrr              0.3.4      2020-04-17 [1] CRAN (R 4.1.1)
 qvalue             2.26.0     2021-10-26 [1] Bioconductor
 R6                 2.5.1      2021-08-19 [1] CRAN (R 4.1.1)
 RColorBrewer       1.1-2      2014-12-07 [1] CRAN (R 4.1.1)
 Rcpp               1.0.7      2021-07-07 [1] CRAN (R 4.1.1)
 RCurl              1.98-1.5   2021-09-17 [1] CRAN (R 4.1.1)
 remotes            2.4.1      2021-09-29 [1] CRAN (R 4.1.1)
 reshape2           1.4.4      2020-04-09 [1] CRAN (R 4.1.1)
 rlang              0.4.12     2021-10-18 [1] CRAN (R 4.1.1)
 rprojroot          2.0.2      2020-11-15 [1] CRAN (R 4.1.1)
 RSQLite            2.2.8      2021-08-21 [1] CRAN (R 4.1.1)
 S4Vectors        * 0.32.2     2021-11-07 [1] Bioconductor
 scales             1.1.1      2020-05-11 [1] CRAN (R 4.1.1)
 scatterpie         0.1.7      2021-08-20 [1] CRAN (R 4.1.1)
 sessioninfo        1.2.1      2021-11-02 [1] CRAN (R 4.1.1)
 shadowtext         0.0.9      2021-09-19 [1] CRAN (R 4.1.1)
 snow               0.4-4      2021-10-27 [1] CRAN (R 4.1.1)
 stringi            1.7.5      2021-10-04 [1] CRAN (R 4.1.1)
 stringr            1.4.0      2019-02-10 [1] CRAN (R 4.1.1)
 testthat           3.1.0      2021-10-04 [1] CRAN (R 4.1.1)
 tibble             3.1.6      2021-11-07 [1] CRAN (R 4.1.1)
 tidygraph          1.2.0      2020-05-12 [1] CRAN (R 4.1.1)
 tidyr              1.1.4      2021-09-27 [1] CRAN (R 4.1.1)
 tidyselect         1.1.1      2021-04-30 [1] CRAN (R 4.1.1)
 tidytree           0.3.6      2021-11-12 [1] CRAN (R 4.1.1)
 treeio             1.18.0     2021-10-26 [1] Bioconductor
 tweenr             1.0.2      2021-03-23 [1] CRAN (R 4.1.1)
 usethis            2.1.3      2021-10-27 [1] CRAN (R 4.1.1)
 utf8               1.2.2      2021-07-24 [1] CRAN (R 4.1.1)
 vctrs              0.3.8      2021-04-29 [1] CRAN (R 4.1.1)
 viridis            0.6.2      2021-10-13 [1] CRAN (R 4.1.1)
 viridisLite        0.4.0      2021-04-13 [1] CRAN (R 4.1.1)
 withr              2.4.3      2021-11-30 [1] CRAN (R 4.1.2)
 XVector            0.34.0     2021-10-26 [1] Bioconductor
 yulab.utils        0.0.4      2021-10-09 [1] CRAN (R 4.1.1)
 zlibbioc           1.40.0     2021-10-26 [1] Bioconductor
BhardwajArch commented 2 years ago

Hello

This is my session info

package version date (UTC) lib source abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.2) AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor ape 5.6-1 2022-01-07 [1] CRAN (R 4.1.2) aplot 0.1.2 2022-01-10 [1] CRAN (R 4.1.2) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.2) backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.2) Biobase 2.54.0 2021-10-26 [1] Bioconductor BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor BiocManager 1.30.16 2021-06-15 [1] CRAN (R 4.1.0) BiocParallel 1.28.3 2021-12-09 [1] Bioconductor Biostrings 2.62.0 2021-10-26 [1] Bioconductor bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.2) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.2) bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.2) blob 1.2.2 2021-07-23 [1] CRAN (R 4.1.2) brio 1.1.3 2021-11-30 [1] CRAN (R 4.1.2) broom 0.7.12 2022-01-28 [1] CRAN (R 4.1.2) cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.2) callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.2) car 3.0-12 2021-11-06 [1] CRAN (R 4.1.0) carData 3.0-5 2022-01-06 [1] CRAN (R 4.1.2) cli 3.1.1 2022-01-20 [1] CRAN (R 4.1.2) clusterProfiler 4.3.2.991 2022-02-07 [1] Github @.) colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.2) crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.2) curl 4.3.2 2021-06-23 [3] CRAN (R 4.1.0) data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.2) DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.2) desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.2) devtools 2.4.3 2021-11-30 [1] CRAN (R 4.1.2) digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.2) DO.db 2.9 2022-02-07 [1] Bioconductor DOSE 3.21.2 2022-02-07 [1] Github @.) downloader 0.4 2015-07-09 [1] CRAN (R 4.1.2) V dplyr 1.0.7 2022-02-08 [1] CRAN (R 4.1.2) (on disk 1.0.8) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2) enrichplot * 1.13.1.992 2022-02-09 [1] Github @.**) fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2) farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.2) fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.2) fastmatch 1.1-3 2021-07-23 [1] CRAN (R 4.1.2) fgsea 1.20.0 2021-10-26 [1] Bioconductor fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.2) generics 0.1.2 2022-01-31 [1] CRAN (R 4.1.2) GenomeInfoDb 1.30.1 2022-01-30 [1] Bioconductor GenomeInfoDbData 1.2.7 2021-11-29 [1] Bioconductor ggforce 0.3.3 2021-03-05 [1] CRAN (R 4.1.2) ggfun 0.0.5 2022-01-20 [1] CRAN (R 4.1.2) ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.1.2) ggplotify 0.1.0 2021-09-02 [1] CRAN (R 4.1.2) ggpubr 0.4.0 2020-06-27 [1] CRAN (R 4.1.0) ggraph 2.0.5 2021-02-23 [1] CRAN (R 4.1.2) ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.1.2) ggsignif 0.6.3 2021-09-09 [1] CRAN (R 4.1.0) ggtree 3.2.1 2021-11-16 [1] Bioconductor glue 1.6.1 2022-01-22 [1] CRAN (R 4.1.2) GO.db 3.14.0 2022-02-07 [1] Bioconductor GOSemSim 2.20.0 2021-10-26 [1] Bioconductor graphlayouts 0.8.0 2022-01-03 [1] CRAN (R 4.1.2) gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.2) gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.1.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.2) httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.2) igraph 1.2.11 2022-01-04 [1] CRAN (R 4.1.2) IRanges 2.28.0 2021-10-26 [1] Bioconductor jsonlite 1.7.3 2022-01-17 [1] CRAN (R 4.1.2) KEGGREST 1.34.0 2021-10-26 [1] Bioconductor labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.2) lattice 0.20-45 2021-09-22 [4] CRAN (R 4.1.1) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.2) lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.2) magrittr 2.0.2 2022-01-26 [1] CRAN (R 4.1.2) MASS 7.3-54 2021-05-03 [4] CRAN (R 4.0.5) Matrix 1.3-4 2021-06-01 [4] CRAN (R 4.1.0) memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.2) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.2) nlme 3.1-152 2021-02-04 [4] CRAN (R 4.0.3) org.Hs.eg.db 3.14.0 2022-01-03 [1] Bioconductor patchwork 1.1.1 2020-12-17 [1] CRAN (R 4.1.2) pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.2) pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.2) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.2) pkgload 1.2.4 2021-11-30 [1] CRAN (R 4.1.2) plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.2) png 0.1-7 2013-12-03 [1] CRAN (R 4.1.2) polyclip 1.10-0 2019-03-14 [1] CRAN (R 4.1.2) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.2) processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.2) ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.2) purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.2) qvalue 2.26.0 2021-10-26 [1] Bioconductor R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.2) RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.2) Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.1.2) V RCurl 1.98-1.5 2022-02-08 [1] CRAN (R 4.1.2) (on disk 1.98.1.6) remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.2) reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.2) rlang 1.0.1 2022-02-03 [1] CRAN (R 4.1.2) rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.2) RSQLite 2.2.9 2021-12-06 [1] CRAN (R 4.1.2) rstatix 0.7.0 2021-02-13 [1] CRAN (R 4.1.0) S4Vectors 0.32.3 2021-11-21 [1] Bioconductor scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.2) scatterpie 0.1.7 2021-08-20 [1] CRAN (R 4.1.2) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2) shadowtext 0.1.1 2022-01-10 [1] CRAN (R 4.1.2) stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.2) stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.2) testthat 3.1.2 2022-01-20 [1] CRAN (R 4.1.2) tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.2) tidygraph 1.2.0 2020-05-12 [1] CRAN (R 4.1.2) tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.1.2) tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.2) tidytree 0.3.7 2022-01-10 [1] CRAN (R 4.1.2) treeio 1.18.1 2021-11-14 [1] Bioconductor tweenr 1.0.2 2021-03-23 [1] CRAN (R 4.1.2) usethis 2.1.5 2021-12-09 [1] CRAN (R 4.1.2) utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.2) vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.2) viridis 0.6.2 2021-10-13 [1] CRAN (R 4.1.2) viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.2) withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.2) XVector 0.34.0 2021-10-26 [1] Bioconductor yulab.utils 0.0.4 2021-10-09 [1] CRAN (R 4.1.2) zlibbioc 1.40.0 2021-10-26 [1] Bioconductor

On Wed, Feb 9, 2022 at 8:54 AM Erqiang Hu @.***> wrote:

@BhardwajArch https://github.com/BhardwajArch Your data work well with the Github version of clusterProfiler, enrichplot and DOSE. Please check your package version. This is my sessioninfo:

devtools::session_info()- Session info -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- hash: backhand index pointing right: medium skin tone, waving hand: dark skin tone, scarf

setting value version R version 4.1.1 (2021-08-10) os Windows 10 x64 (build 18363) system x86_64, mingw32 ui Rgui language (EN) collate Chinese (Simplified)_China.936 ctype Chinese (Simplified)_China.936 tz Asia/Taipei date 2022-02-09 pandoc 2.10.1 @ C:\Users\Dell\AppData\Local\Pandoc\pandoc.exe

  • Packages ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- package version date (UTC) lib source AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor ape 5.5 2021-04-25 [1] CRAN (R 4.1.1) aplot 0.1.1 2021-09-22 [1] CRAN (R 4.1.1) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.1) Biobase 2.54.0 2021-10-26 [1] Bioconductor BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor BiocParallel 1.28.0 2021-10-26 [1] Bioconductor Biostrings 2.62.0 2021-10-26 [1] Bioconductor bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.1) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.1) bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.1) blob 1.2.2 2021-07-23 [1] CRAN (R 4.1.1) cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.1) callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.1) cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.1) clusterProfiler 4.3.2.991 2022-01-27 [1] Bioconductor colorspace 2.0-2 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0.0.5 2022-01-20 [1] CRAN (R 4.1.2) ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.1.1) ggplotify 0.1.0 2021-09-02 [1] CRAN (R 4.1.1) ggraph 2.0.5 2021-02-23 [1] CRAN (R 4.1.1) ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.1.1) ggtree 3.2.0 2021-10-26 [1] Bioconductor glue 1.5.0 2021-11-07 [1] CRAN (R 4.1.1) GO.db 3.14.0 2021-11-13 [1] Bioconductor GOSemSim 2.20.0 2021-10-26 [1] Bioconductor graphlayouts 0.7.2 2021-11-21 [1] CRAN (R 4.1.2) gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.1) gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.1.1) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.1) httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.1) igraph 1.2.7 2021-10-15 [1] CRAN (R 4.1.1) IRanges 2.28.0 2021-10-26 [1] Bioconductor jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.1) KEGGREST 1.34.0 2021-10-26 [1] Bioconductor lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.1) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.1) lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1) magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.1) MASS 7.3-54 2021-05-03 [1] CRAN (R 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BhardwajArch commented 2 years ago

I have all updated version of required packages but I am getting error for visualization

result.out <- enrichplot::pairwise_termsim(res_out) Error in $<-.data.frame(tmp, "Cluster", value = NAinteger) :

On Wed, Feb 9, 2022 at 11:42 AM Archana Bhardwaj @.***> wrote:

Hello

This is my session info

package version date (UTC) lib source abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.2) AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor ape 5.6-1 2022-01-07 [1] CRAN (R 4.1.2) aplot 0.1.2 2022-01-10 [1] CRAN (R 4.1.2) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.2) backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.2) Biobase 2.54.0 2021-10-26 [1] Bioconductor BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor BiocManager 1.30.16 2021-06-15 [1] CRAN (R 4.1.0) BiocParallel 1.28.3 2021-12-09 [1] Bioconductor Biostrings 2.62.0 2021-10-26 [1] Bioconductor bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.2) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.2) bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.2) blob 1.2.2 2021-07-23 [1] CRAN (R 4.1.2) brio 1.1.3 2021-11-30 [1] CRAN (R 4.1.2) broom 0.7.12 2022-01-28 [1] CRAN (R 4.1.2) cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.2) callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.2) car 3.0-12 2021-11-06 [1] CRAN (R 4.1.0) carData 3.0-5 2022-01-06 [1] CRAN (R 4.1.2) cli 3.1.1 2022-01-20 [1] CRAN (R 4.1.2) clusterProfiler 4.3.2.991 2022-02-07 [1] Github @.) colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.2) crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.2) curl 4.3.2 2021-06-23 [3] CRAN (R 4.1.0) data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.2) DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.2) desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.2) devtools 2.4.3 2021-11-30 [1] CRAN (R 4.1.2) digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.2) DO.db 2.9 2022-02-07 [1] Bioconductor DOSE 3.21.2 2022-02-07 [1] Github @.) downloader 0.4 2015-07-09 [1] CRAN (R 4.1.2) V dplyr 1.0.7 2022-02-08 [1] CRAN (R 4.1.2) (on disk 1.0.8) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2) enrichplot * 1.13.1.992 2022-02-09 [1] Github @.**) fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2) farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.2) fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.2) fastmatch 1.1-3 2021-07-23 [1] CRAN (R 4.1.2) fgsea 1.20.0 2021-10-26 [1] Bioconductor fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.2) generics 0.1.2 2022-01-31 [1] CRAN (R 4.1.2) GenomeInfoDb 1.30.1 2022-01-30 [1] Bioconductor GenomeInfoDbData 1.2.7 2021-11-29 [1] Bioconductor ggforce 0.3.3 2021-03-05 [1] CRAN (R 4.1.2) ggfun 0.0.5 2022-01-20 [1] CRAN (R 4.1.2) ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.1.2) ggplotify 0.1.0 2021-09-02 [1] CRAN (R 4.1.2) ggpubr 0.4.0 2020-06-27 [1] CRAN (R 4.1.0) ggraph 2.0.5 2021-02-23 [1] CRAN (R 4.1.2) ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.1.2) ggsignif 0.6.3 2021-09-09 [1] CRAN (R 4.1.0) ggtree 3.2.1 2021-11-16 [1] Bioconductor glue 1.6.1 2022-01-22 [1] CRAN (R 4.1.2) GO.db 3.14.0 2022-02-07 [1] Bioconductor GOSemSim 2.20.0 2021-10-26 [1] Bioconductor graphlayouts 0.8.0 2022-01-03 [1] CRAN (R 4.1.2) gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.2) gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.1.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.2) httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.2) igraph 1.2.11 2022-01-04 [1] CRAN (R 4.1.2) IRanges 2.28.0 2021-10-26 [1] Bioconductor jsonlite 1.7.3 2022-01-17 [1] CRAN (R 4.1.2) KEGGREST 1.34.0 2021-10-26 [1] Bioconductor 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CRAN (R 4.1.2) qvalue 2.26.0 2021-10-26 [1] Bioconductor R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.2) RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.2) Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.1.2) V RCurl 1.98-1.5 2022-02-08 [1] CRAN (R 4.1.2) (on disk 1.98.1.6) remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.2) reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.2) rlang 1.0.1 2022-02-03 [1] CRAN (R 4.1.2) rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.2) RSQLite 2.2.9 2021-12-06 [1] CRAN (R 4.1.2) rstatix 0.7.0 2021-02-13 [1] CRAN (R 4.1.0) S4Vectors 0.32.3 2021-11-21 [1] Bioconductor scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.2) scatterpie 0.1.7 2021-08-20 [1] CRAN (R 4.1.2) sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2) shadowtext 0.1.1 2022-01-10 [1] CRAN (R 4.1.2) stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.2) stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.2) testthat 3.1.2 2022-01-20 [1] CRAN (R 4.1.2) tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.2) tidygraph 1.2.0 2020-05-12 [1] CRAN (R 4.1.2) tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.1.2) tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.2) tidytree 0.3.7 2022-01-10 [1] CRAN (R 4.1.2) treeio 1.18.1 2021-11-14 [1] Bioconductor tweenr 1.0.2 2021-03-23 [1] CRAN (R 4.1.2) usethis 2.1.5 2021-12-09 [1] CRAN (R 4.1.2) utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.2) vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.2) viridis 0.6.2 2021-10-13 [1] CRAN (R 4.1.2) viridisLite 0.4.0 2021-04-13 [1] CRAN (R 4.1.2) withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.2) XVector 0.34.0 2021-10-26 [1] Bioconductor yulab.utils 0.0.4 2021-10-09 [1] CRAN (R 4.1.2) zlibbioc 1.40.0 2021-10-26 [1] Bioconductor

On Wed, Feb 9, 2022 at 8:54 AM Erqiang Hu @.***> wrote:

@BhardwajArch https://github.com/BhardwajArch Your data work well with the Github version of clusterProfiler, enrichplot and DOSE. Please check your package version. This is my sessioninfo:

devtools::session_info()- Session info -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- hash: backhand index pointing right: medium skin tone, waving hand: dark skin tone, scarf

setting value version R version 4.1.1 (2021-08-10) os Windows 10 x64 (build 18363) system x86_64, mingw32 ui Rgui language (EN) collate Chinese (Simplified)_China.936 ctype Chinese (Simplified)_China.936 tz Asia/Taipei date 2022-02-09 pandoc 2.10.1 @ C:\Users\Dell\AppData\Local\Pandoc\pandoc.exe

  • Packages ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- package version date (UTC) lib source AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor ape 5.5 2021-04-25 [1] CRAN (R 4.1.1) aplot 0.1.1 2021-09-22 [1] CRAN (R 4.1.1) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.1) Biobase 2.54.0 2021-10-26 [1] Bioconductor BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor BiocParallel 1.28.0 2021-10-26 [1] Bioconductor Biostrings 2.62.0 2021-10-26 [1] Bioconductor bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.1) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.1) bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.1) blob 1.2.2 2021-07-23 [1] CRAN (R 4.1.1) cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.1) callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.1) cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.1) clusterProfiler 4.3.2.991 2022-01-27 [1] Bioconductor colorspace 2.0-2 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huerqiang commented 2 years ago

@BhardwajArch Update your enrichplot(Version: 1.15.2.900).