Open martinezvbs opened 6 months ago
Hi, I think I was able to reproduce this error. It seems to come from having too few colors configured for the the number of items.
I just pushed a fix. Reinstall from github and try again please., You should see ssvQC version 1.0.22.
With the code you have, it will reuse the same 8 colors. You'd have more control if you made config objects before creating the ssvQC object. QcConfigFeatures.files and QcConfigSignal.files are the relevant functions.
From the help : ?QcConfigSignal.files
object2 = QcConfigSignal.files(bam_files, sample_names = c("MCF10A_CTCF", "MCF10AT1_CTCF", "MCF10CA1a_CTCF"), group_names = c("10A", "AT1", "CA1"), group_colors = c("firebrick", "slategray2", "forestgreen") )
Hi,
Thanks for the quick response, it is working now (:
One more question, I was running the following code to access to the plots
sqc$plots$signal
sqc$plots$features$venn
sqc$plots$correlation$signal_profile_ggplot_heatmap
Again, thanks for the time!
I'm kind of guessing what you're looking at here based on the info you've provided. My guess is that ssvQC is looking at each peak set individually in the context of all signals files for each.
If what you wanted is a comparison between all your peak sets, then give the following code a try:
qcf = QcConfigFeatures.files(np_files, run_separately = FALSE)
sqc = ssvQC(qcf, bw_files)
By going through a config object we have much more control.
Also since you have so many peak sets, a venn diagram is unlikely to helpful, and ssvQC can't create a venn for that many anyway.
I'd recommend:
sqc$plots$features$binary_heatmap$All_features
sqc$plots$features$UpSet$All_features
Hi,
Yes, the recommendation above worked,
thank you so much!
Hi,
I am new using the tool and I was following the description on the main page using
Then when I try to run
I got the following message
More info about the input files
Any advise?
Thanks!