ds_plots.R | Error in if (pos < min(s)) my_xlim[1] else if (pos > max(s)) my_xlim[2] else {

[yenon118]

Hi,

I was trying to generate the PDF file using the ds_plots.R script. However, the output PDF was empty and I received the error messages below. Does anybody know what is the possible cause of this error?

The command:

Rscript ../../../../tools/leafcutter/scripts/ds_plots.R \
-f 0.05 \
-o "2023_06_16_res_group_file__AR_A_U_Input__WT_A_U_Input.pdf" \
-e ../output/Mus_musculus.GRCm39.107.txt.gz \
../output/2023_06_10_run_Intron_Clustering/testYRIvsEU_perind_numers.counts.gz \
../data/2023_06_15_run_Leafcutter_ds/group_file__AR_A_U_Input__WT_A_U_Input.txt \
../output/2023_06_16_run_Leafcutter_ds/group_file__AR_A_U_Input__WT_A_U_Input/2023_06_16_group_file__AR_A_U_Input__WT_A_U_Input__cluster_significance.txt

The output:

Loading required package: Rcpp
Loading counts from ../output/2023_06_10_run_Intron_Clustering/testYRIvsEU_perind_numers.counts.gz 
Loading metadata from ../data/2023_06_15_run_Leafcutter_ds/group_file__AR_A_U_Input__WT_A_U_Input.txt 
Loading exons from ../output/Mus_musculus.GRCm39.107.txt.gz 
Saving 22 plots to 2023_06_16_res_group_file__AR_A_U_Input__WT_A_U_Input.pdf 
[1] "chr1:clu_3802_+"
[1] AR_A_U_Input
Levels: AR_A_U_Input WT_A_U_Input
 [1]  1 40  7  8  2  6  2 10 27 21  4  2  8
[1] WT_A_U_Input
Levels: AR_A_U_Input WT_A_U_Input
 [1] 13 14  5 10  0 11  0  0 29 26  5  8 21
Error in if (pos < min(s)) my_xlim[1] else if (pos > max(s)) my_xlim[2] else { : 
  missing value where TRUE/FALSE needed
Calls: make_differential_splicing_plot -> data.frame -> sapply -> lapply -> FUN
Execution halted