Entering edit mode
Hi,
I am running gene set enrichment analysis on R using the fgsea
package and plotting the results using ggplot
. The main code for plotting the results is as follows:
ggplot(fgseaRes_sig, aes(reorder(pathway, NES), NES)) +
geom_col(aes(fill=padj<0.1)) +
coord_flip() +
labs(x="Pathway", y="Normalized Enrichment Score",
title=fig_title) +
theme_minimal() +
theme(axis.text.y = element_text(colour = a))
I ran this code previously and it worked fine. However, when I run it now, it gives the following error:
Error in ggplot(fgseaRes_sig, aes(reorder(pathway, NES), NES)) + geom_col(aes(fill = padj < :
could not find function "+<-"
It seems that ggplot doesn't get that I want to use the comparator '<'? And it's confusing it for a tidyverse function perhaps?
Here is my sessionInfo():
sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.14.0 fgsea_1.21.0 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[6] purrr_0.3.4 readr_2.0.1 tidyr_1.1.3 tibble_3.1.4 ggplot2_3.3.5
loaded via a namespace (and not attached):
[1] tidyselect_1.1.1 haven_2.4.3 lattice_0.20-45 colorspace_2.0-2
[5] vctrs_0.3.8 generics_0.1.0 utf8_1.2.2 rlang_0.4.12
[9] pillar_1.6.3 glue_1.4.2 withr_2.4.2 DBI_1.1.1
[13] BiocParallel_1.27.10 dbplyr_2.1.1 modelr_0.1.8 readxl_1.3.1
[17] lifecycle_1.0.1 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0
[21] rvest_1.0.1 tzdb_0.1.2 parallel_4.1.1 fansi_0.5.0
[25] broom_0.7.9 Rcpp_1.0.7 scales_1.1.1 backports_1.2.1
[29] jsonlite_1.7.2 fs_1.5.0 gridExtra_2.3 fastmatch_1.1-3
[33] hms_1.1.1 stringi_1.7.4 grid_4.1.1 cli_3.0.1
[37] tools_4.1.1 magrittr_2.0.1 crayon_1.4.1 pkgconfig_2.0.3
[41] ellipsis_0.3.2 Matrix_1.3-4 xml2_1.3.2 reprex_2.0.1
[45] lubridate_1.7.10 assertthat_0.2.1 httr_1.4.2 rstudioapi_0.13
[49] R6_2.5.1 compiler_4.1.1