Hello,

All the codes are running well.

I tried to plot the enrichment of the GSEA. But it comes out the error.

Thank you in advance for great help!

Best,

Yue

> library(fgsea)
> library(tidyverse)
> library(data.table)
> library(ggplot2)
> setwd("/media/hp/04c65089-71ff-4b33-9a30-c21b8c77eda2/li/HASM_SILAC/finally/DEP")
> #AC6_vs_lacZ
> res<-read.table("AC6_vs_lacZ_fgsea.txt")
> ranks <- deframe(res)
> pathways.kegg<- gmtPathways("c2.cp.kegg.v7.2.symbols.gmt")
> fgseaRes_kegg<- fgsea(pathways = pathways.kegg, stats  = ranks,  minSize = 1,maxSize  = Inf)
Warning message:
In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
There are ties in the preranked stats (1.13% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
> fwrite(fgseaRes_kegg, file="AC6_vs_lacZ_kegg.txt", sep="\t", sep2=c("", " ", ""))

> plotEnrichment(pathways.kegg[["KEGG_PYRIMIDINE_METABOLISM"]],
+                exampleRanks) 
 Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
 Run `rlang::last_error()` to see where the error occurred.
 In addition: Warning messages:
1: In max(tops) : no non-missing arguments to max; returning -Inf
2: In min(bottoms) : no non-missing arguments to min; returning Inf
3: In max(tops) : no non-missing arguments to max; returning -Inf
4: In min(bottoms) : no non-missing arguments to min; returning Inf
5: In max(tops) : no non-missing arguments to max; returning -Inf
6: In min(bottoms) : no non-missing arguments to min; returning Inf


> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

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_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] devtools_2.3.2       usethis_2.0.1        org.Hs.eg.db_3.12.0  AnnotationDbi_1.52.0 IRanges_2.24.1       S4Vectors_0.28.1    
 [7] Biobase_2.50.0       BiocGenerics_0.36.0  BiocParallel_1.24.1  forcats_0.5.1        stringr_1.4.0        dplyr_1.0.4         
[13] purrr_0.3.4          readr_1.4.0          tidyr_1.1.2          tibble_3.1.0         tidyverse_1.3.0      ggplot2_3.3.3       
[19] data.table_1.14.0    fgsea_1.17.1        

loaded via a namespace (and not attached):
 [1] fs_1.5.0            lubridate_1.7.10    bit64_4.0.5         httr_1.4.2          rprojroot_2.0.2     tools_4.0.4        
 [7] backports_1.2.1     utf8_1.1.4          R6_2.5.0            DBI_1.1.1           colorspace_2.0-0    withr_2.4.1        
[13] tidyselect_1.1.0    gridExtra_2.3       prettyunits_1.1.1   processx_3.4.5      bit_4.0.4           curl_4.3           
[19] compiler_4.0.4      cli_2.3.1           rvest_0.3.6         xml2_1.3.2          desc_1.2.0          labeling_0.4.2     
[25] scales_1.1.1        callr_3.5.1         digest_0.6.27       pkgconfig_2.0.3     sessioninfo_1.1.1   dbplyr_2.1.0       
[31] fastmap_1.1.0       rlang_0.4.10        readxl_1.3.1        rstudioapi_0.13     RSQLite_2.2.3       farver_2.0.3       
[37] generics_0.1.0      jsonlite_1.7.2      magrittr_2.0.1      Matrix_1.3-2        Rcpp_1.0.6          munsell_0.5.0      
[43] fansi_0.4.2         lifecycle_1.0.0     stringi_1.5.3       pkgbuild_1.2.0      grid_4.0.4          blob_1.2.1         
[49] crayon_1.4.1        lattice_0.20-41     haven_2.3.1         hms_1.0.0           ps_1.5.0            pillar_1.5.0       
[55] pkgload_1.2.0       fastmatch_1.1-0     reprex_1.0.0        glue_1.4.2          remotes_2.2.0       BiocManager_1.30.10
[61] modelr_0.1.8        vctrs_0.3.6         testthat_3.0.2      cellranger_1.1.0    gtable_0.3.0        assertthat_0.2.1   
[67] cachem_1.0.4        broom_0.7.5         memoise_2.0.0       ellipsis_0.3.1     

` ```

I knew what I am wrong .

plotEnrichment(pathways.kegg[["KEGG_PYRIMIDINE_METABOLISM"]],   ranks) 

It should be "ranks", not exampleRanks.