How to show uncertainty, error bars, or multiple lines?

[deeptools]

How to show uncertainty, error bars, or multiple lines?

[vivekbhr]

Hi @slowkow . Maybe I can help.

One example of such file is here. It's referred as [bedgraph matrix] in the config. Basically, it's a bedgraph file (chr, start, end, score) with extra columns for scores from replicates.

For additional information on config files, the current hicPlotTADs documentation might be helpful. Additionally, config files with some explanation of fields can directly be generated from a list of files using make_tracks_file. Genes can be represented as bed6 or bed12 files at this moment.

[fidelram]

I added a new example to the README.md Maybe that helps.

[slowkow]

Hi Fidel, that's a great example. Could I ask you to please share the configuration?

I guess the gray lines are plotted with a configuration that looks something like this:

[bedgraph matrix]
# a bedgraph matrix file is like a bedgraph, except that per bin there
# are more than one value separated by tab: E.g.
# chrX       18279   40131   0.399113        0.364118        0.320857        0.274307
# chrX       40132   54262   0.479340        0.425471        0.366541        0.324736
# bedgraph matrices are produced by hicFindTADs
file = spectra_conductance.bm
title = conductance spectra
width = 1.5
orientation = inverted
min_value = 0.10
max_value = 0.70
# if type is set as lines, then the TAD score lines are drawn instead
# of the matrix
# set to lines if a heatmap representing the matrix
# is not wanted
type = lines
file_type = bedgraph_matrix

For the mean, are you creating an additional bedgraph file and then plotting it? What does the configuration look like for that?

[fidelram]

Yes, the configuration looks like that. When you use the bedgraph_matrix file_type, the mean is computed based on the data. No extra file is needed.

[werhmk]

hi,Fidel,
how to handle with a GFF3 file, should it be convert to BED file?
thanks.

[bgruening]

Hi @werhmk!

Please try the latest release - it has gtf support: https://github.com/deeptools/pyGenomeTracks/releases/tag/3.1 That should hopefully work.