longjp
commented
2 years ago For completeness, I include plots from the MWE above and the output from running the script.
Good plot:
Bad plot:
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> library(enrichR)
Welcome to enrichR
Checking connection ...
Enrichr ... Connection is Live!
FlyEnrichr ... Connection is available!
WormEnrichr ... Connection is available!
YeastEnrichr ... Connection is available!
FishEnrichr ... Connection is available!
OxEnrichr ... Connection is available!
Warning message:
package ‘enrichR’ was built under R version 4.1.3
> df <- data.frame(Term=c("Pathway 1 with similar name",
+ "Pathway 1 with similar name but slighly different",
+ "Pathway 3",
+ "Pathway 4"),
+ Overlap=c("10/15","15/20","1/10","3/30"),
+ P.value=c(0.0001,0.0002,0.3,0.5))
> # works because all pathways have unique names when truncated to 40 characters
> plotEnrich(df,showTerms=3,
+ numChar = 40,y="Ratio",
+ orderBy="P.value",
+ title="Title")
> # fails because bars from two pathways with similar names are merged together
> plotEnrich(df,showTerms=3,
+ numChar = 20,y="Ratio",
+ orderBy="P.value",
+ title="Title")
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Users/jplong/opt/miniconda3/lib/libopenblasp-r0.3.18.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] enrichR_3.1
loaded via a namespace (and not attached):
[1] magrittr_2.0.1 tidyselect_1.1.1 munsell_0.5.0 colorspace_2.0-2 rjson_0.2.20 R6_2.5.1 rlang_0.4.12
[8] fansi_0.5.0 httr_1.4.2 dplyr_1.0.7 tools_4.1.1 grid_4.1.1 gtable_0.3.0 utf8_1.2.2
[15] DBI_1.1.1 ellipsis_0.3.2 digest_0.6.28 assertthat_0.2.1 tibble_3.1.6 lifecycle_1.0.1 crayon_1.4.2
[22] farver_2.1.0 purrr_0.3.4 ggplot2_3.3.5 vctrs_0.3.8 curl_4.3.2 glue_1.5.0 labeling_0.4.2
[29] compiler_4.1.1 pillar_1.6.4 generics_0.1.1 scales_1.1.1 pkgconfig_2.0.3 
ycl6
wjawaid
plotEnrich produces a bar for each unique pathway name after truncating pathway name to numChar. However since several pathways have similar names (same leading 40 characters), this can result in the bars of different pathways being added together (ggplot2 default). In an application I am working on, I had a Gene Ratio of over 1 on the plot, which is impossible. Below is a MWE with fake data. I believe enforcing unique truncated pathway names would fix the issue:
On a project with real data I got this: