plotRuns produces an unreadble file.pdf

[matteomaster]

Hi everyone,
I'm working on a project for my MSc Thesis in Population Genomics to produce RoH and RoHet with R package "detectRUNS".

I used "slidingRUNS.run()" function and it seems work, looking at the output;
then I used plotRuns() to save and see the graphics produces, but, like said in the title, plotRuns produces an unreadble file.pdf. Whenever I try to open it says "impossible to open file.pdf: it is possible that the file is damaged, or its format is unrecognized".

I am working on macOS Monterey 12.0.1, and Rstudio v. 4.2.2, and detectRUNS v. 0.9.6

the followed steps represent my code:

library(detectRUNS)

genotypeFilePath <- "dati/MMC1_notab.ped"
mapFilePath <- "dati/MMC1_fixed.map"

slidingRuns <- slidingRUNS.run(
genotypeFile = genotypeFilePath,
mapFile = mapFilePath,
windowSize = 15,
threshold = 0.01,
minSNP = 5,
ROHet = FALSE,
maxOppWindow = 1,
maxMissWindow = 1,
maxGap = 10^6,
minLengthBps = 250000,
minDensity = 1/1000, # SNP/kbps
maxOppRun = NULL,
maxMissRun = NULL
)

plot_Runs(runs = slidingRuns,
suppressInds = FALSE,
savePlots = TRUE,
outputName = "RoH")

the output of head(slidingRuns) looks like this:

group        id            chrom         nSNP     start           end              length

Wolf_11 | Wolf_11 | 994383.1 | 1112 | 6456102 | 6874518 | 412916
Wolf_11 | Wolf_11 | 994383.1 | 1162 | 12055005 | 124596395 | 404090
Wolf_11 | Wolf_11 | 994383.1 | 323 | 22510224 | 27845146 | 334522

Thank you for the answers!

[bunop]

Dear @matteomaster ,

thank you for your interest in detectRUNS. Regarding your question, I think that the problem are chromosome names, which are expected to be numerical as plink does without the option --extra-chrom, as you can see here.

Can you rename your chromosomes with integers from 0 to 99 and try to save a plot?

[bunop]

moreover, I'm not sure that this function can work as expected with the header like you put in your first comment, since it expect columns name like "group" "id" "chrom" "nSNP" "from" "to" "lengthBps", or at least from and to instead from start and stop, since these columns are required to make intervals