The following error was spotted when trying to run the makeGraph.R: https://github.com/nf-core/sarek/issues/993
When trying the suggested solution of running the makeGraph2.0.R script, the issue persisted.
Digging deeper into the issue, It was spotted that the cause were NaN values being produced when calculating the log2 of the ratio, which triggered the error: "Error in plot.window(...) : need finite 'ylim' values"
The changes introduced do the following:
Added a column to the table that contains the calculated log2 values of the ratio.
This column is now used to filter the table, so that rows with NaN log2 values are removed when iterating through the chromosomes to generate the plot.
Updated the plot command line so that it uses this column, instead of calculating the log2 value with each iteration.
I compared the files produced by makeGraph.R and the ones produced by this version of makeGraph2.0.R and the plots they produced were identical. Attaching them below, keep in mind that the missing text in "HCC1395T_vs_HCC1395N_ratio log2_makeGraph", is due to an unrelated issue in the sarek's pipeline: https://github.com/nf-core/sarek/issues/921
The following error was spotted when trying to run the makeGraph.R: https://github.com/nf-core/sarek/issues/993 When trying the suggested solution of running the makeGraph2.0.R script, the issue persisted. Digging deeper into the issue, It was spotted that the cause were NaN values being produced when calculating the log2 of the ratio, which triggered the error: "Error in plot.window(...) : need finite 'ylim' values"
The changes introduced do the following:
I compared the files produced by makeGraph.R and the ones produced by this version of makeGraph2.0.R and the plots they produced were identical. Attaching them below, keep in mind that the missing text in "HCC1395T_vs_HCC1395N_ratio log2_makeGraph", is due to an unrelated issue in the sarek's pipeline: https://github.com/nf-core/sarek/issues/921