Issue executing pafCoordsDotPlotly.R

[jsromanowski]

Hello all,

I have downloaded pafCoordsDotPlotly.R and have created a .paf file with my two .fa files using minimap2.
I am now trying to create my dot plot, however I am having issues executing pafCoordsDotPlotly.R in my terminal.

I used the following command:

"pafCoordsDotPlotly.R -i AaegL5.chrom1.minimap2.paf -o AaegL5.chrom1.plot -s -t 95"

I receive the following error:

"pafCoordsDotPlotly.R: command not found"

note: I am operating in the directory where the pafCoordsDotPlotly.R script is saved.

Any idea how to fix this?
Thanks

[emistasis]

I know this issue is almost a year old, but I figured I'd drop in with a possible way to resolve it in case any future users run into it.

My recommendation is to just run the script within RStudio. Make sure that you install the necessary packages beforehand, and then you should be able to run the script as follows:

install.packages(c("optparse", "ggplot2", "plotly"))

DotPlotly_lines <- paste("Rscript",
                         "pafCoordsDotPlotly.R",
                         "-i input.paf",
                         "-o output",
                         "-s",
                         "-t")
system(DotPlotly_lines)

Hope this helps!

[lonelyjoeparker]

It's a decent workaround. Would be helpful if the OP @jsromanowski posted OS and shell information to reproduce the error tho, plus ideally whether they've been able to run the example files and it's just their .paf which aren't working.

[lonelyjoeparker]

@emistasis if you're in contact with @tpoorten could you ask them to have a look at my PR #23 for issue #18 ? Ta!