I followed the alternative protocol to obtain the PSI from my bam files and I think everything run fine. The output looks like this (but with the first row with the col names):
001:ENSMUST00000000001 2037 16671 0 1
001:ENSMUST00000000003 1 0 0 NA
001:ENSMUST00000000010 66 2 0 1
001:ENSMUST00000000028 6 1 0 1
001:ENSMUST00000000137 2556 29001 3 0.997852
001:ENSMUST00000000153 1785 15236 0 1
Now, I am trying to visualize the psi results, here I modify the code with the respective directories:
Import plotting main functions
source("~/Splicing/PSI/psi_plot_vis.r")
the location of sampleTable, which provide sample name and grouping factor information
And, when I plot, I got this error:
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
Could this error be related to the psi files? Are the NA values normal?
Any clue will be appreciated
Thanks!
Hi,
I followed the alternative protocol to obtain the PSI from my bam files and I think everything run fine. The output looks like this (but with the first row with the col names): 001:ENSMUST00000000001 2037 16671 0 1 001:ENSMUST00000000003 1 0 0 NA 001:ENSMUST00000000010 66 2 0 1 001:ENSMUST00000000028 6 1 0 1 001:ENSMUST00000000137 2556 29001 3 0.997852 001:ENSMUST00000000153 1785 15236 0 1
Now, I am trying to visualize the psi results, here I modify the code with the respective directories:
Import plotting main functions
source("~/Splicing/PSI/psi_plot_vis.r")
the location of sampleTable, which provide sample name and grouping factor information
Which can be mordified based on need
sampleTablePath = "~/Splicing/PSI/sampleTable.csv"
the path to the psi result fold, the result file should be output directortly from psi.sh script
noted that the end '/' shoubd be included
psiFolder ="~/Splicing/PSI/Aorta_psi/"
the path to the exonic part matrix
exonicPartMatrixPath ="~/Splicing/PSI/Mus_musculus.GRCm39.108.chr_reduce.gtf"
the gene_id which you want to plot
gene_id = "ENSMUST00000000010"
if only plot the mean of each group
as.group = TRUE
calling the following function sequentilly
psiTable <- importPSI(sampleTablePath, psiFolder) geneAnnot <- getGenesAnot(gene_id, exonicPartMatrixPath) genePsi <- getGenesPsi(gene_id = gene_id, psiTable = psiTable, sampleTablePath = sampleTablePath, as.group = TRUE)
ploting the psi
plot(psiPlot(geneAnnot, gene_id, genePsi))
And, when I plot, I got this error: Error in plot.window(...) : need finite 'xlim' values In addition: Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf 3: In min(x) : no non-missing arguments to min; returning Inf 4: In max(x) : no non-missing arguments to max; returning -Inf
Could this error be related to the psi files? Are the NA values normal? Any clue will be appreciated Thanks!