enrichplot
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Error when splitting treeplot
library(clusterProfiler)
data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]
ego3 <- gseGO(geneList = geneList,
OrgDb = org.Hs.eg.db,
ont = "CC",
minGSSize = 100,
maxGSSize = 500,
pvalueCutoff = 0.05,
verbose = FALSE)
If I want to split a resulting plot by the NES sign, this works:
dotplot(ego3, showCategory=25, split=".sign") + facet_grid(.~.sign)
But this does not:
treeplot(ego3, showCategory=25, split=".sign") + facet_grid(.~.sign)
Error in `combine_vars()`:
! At least one layer must contain all faceting variables: `.sign`.
* Plot is missing `.sign`
* Layer 1 is missing `.sign`
* Layer 2 is missing `.sign`
* Layer 3 is missing `.sign`
* Layer 4 is missing `.sign`
* Layer 5 is missing `.sign`
* Layer 6 is missing `.sign`
* Layer 7 is missing `.sign`
* Layer 8 is missing `.sign`
* Layer 9 is missing `.sign`
Run `rlang::last_error()` to see where the error occurred.
Warning message:
Ignoring unknown parameters: align
Backtrace:
1. base `<fn>`(x)
2. ggplot2:::print.ggplot(x)
4. ggplot2:::ggplot_build.ggplot(x)
5. layout$setup(data, plot$data, plot$plot_env)
6. ggplot2 f(..., self = self)
7. self$facet$compute_layout(data, self$facet_params)
8. ggplot2 f(...)
9. ggplot2::combine_vars(data, params$plot_env, cols, drop = params$drop)
Run `rlang::last_trace()` to see the full context.
Any fix for this?
sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 21.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_GB.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] enrichplot_1.15.3 org.Hs.eg.db_3.12.0 AnnotationDbi_1.52.0 IRanges_2.24.1 S4Vectors_0.28.1 clusterProfiler_3.18.1 DOSE_3.16.0 SeuratObject_4.0.4
[9] Biobase_2.50.0 BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] nlme_3.1-152 ggtree_2.4.2 bit64_4.0.5 RColorBrewer_1.1-2 tools_4.0.4 utf8_1.2.2 R6_2.5.1 lazyeval_0.2.2 DBI_1.1.2 colorspace_2.0-3
[11] tidyselect_1.1.2 gridExtra_2.3 bit_4.0.4 compiler_4.0.4 cli_3.2.0 scatterpie_0.1.7 labeling_0.4.2 shadowtext_0.1.1 scales_1.1.1 stringr_1.4.0
[21] digest_0.6.29 yulab.utils_0.0.4 pkgconfig_2.0.3 fastmap_1.1.0 rlang_1.0.2 rstudioapi_0.13 RSQLite_2.2.10 gridGraphics_0.5-1 farver_2.1.0 generics_0.1.2
[31] jsonlite_1.8.0 BiocParallel_1.24.1 GOSemSim_2.16.1 dplyr_1.0.8 magrittr_2.0.2 ggplotify_0.1.0 GO.db_3.12.1 patchwork_1.1.1 Matrix_1.4-0 Rcpp_1.0.8.2
[41] munsell_0.5.0 fansi_1.0.2 ggnewscale_0.4.6 ape_5.6-2 viridis_0.6.2 lifecycle_1.0.1 stringi_1.7.6 ggraph_2.0.5 MASS_7.3-53.1 plyr_1.8.6
[51] qvalue_2.22.0 grid_4.0.4 blob_1.2.2 ggrepel_0.9.1 DO.db_2.9 crayon_1.5.0 lattice_0.20-41 graphlayouts_0.8.0 splines_4.0.4 pillar_1.7.0
[61] fgsea_1.16.0 igraph_1.2.11 reshape2_1.4.4 fastmatch_1.1-3 glue_1.6.2 ggfun_0.0.5 downloader_0.4 data.table_1.14.2 BiocManager_1.30.16 treeio_1.14.4
[71] vctrs_0.3.8 tweenr_1.0.2 gtable_0.3.0 purrr_0.3.4 polyclip_1.10-0 tidyr_1.2.0 assertthat_0.2.1 cachem_1.0.6 ggplot2_3.3.5 ggforce_0.3.3
[81] tidygraph_1.2.0 tidytree_0.3.9 viridisLite_0.4.0 tibble_3.1.6 aplot_0.1.2 rvcheck_0.1.8 memoise_2.0.1 ellipsis_0.3.2
@TJonCooper The treeplot does not support faceting yet.