itx - #95
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| #ax, c = pltchrbox(ax, agpdata[genome.n][chrgrps[chrs[i]][s]], centrodata[genome.n][chrgrps[chrs[i]][s]], indents[s]-offset, genome.lc, chrwidth, minl=minl) | ||
| ax, c = pltchrbox(ax, v, indents[s] - offset, genome.lc, chrwidth, maxl=chrlength, minl=minl) | ||
| elif itx: | ||
| MCHR = cfg['marginchr'] |
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Currently, the margins are customisable. I dont see how they are being customised within the PR.
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I assume that the plotsr.py file would also have some changes but that file does not seem to be part of it PR. |
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Hi Yuying, is the PR still open/what exactly is being implemented? I'm currently updating plotsr a bit and merging Jonas' PR, we aim to have a new release sometime next week. Cheers, |
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Hi Leon, Great that you are working on this! This PR contains some code cleaning, modifications in tutorial files, and an addition of the itx functionality, so chromosome boxes can be drawn left/middle/right/equidistantly aligned. Please let me know if there are problems. Kind regards, |
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What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)
Implemented four itxalign modes.
Cleaned code, removed redundancies.
Added clarifications to files such as markers.bed.
What is the current behavior? (You can also link to an open issue here)
Users can only plot homologous chromosomes in pairs without a means to visualize interchromosomal structural variations.
What is the new behavior (if this is a feature change)?
Users can plot chromosomes side by side and genomes in pair to visualize interchromosomal structural variations with the new itxalign feature.
Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)
Users do not need to change the command line. However, if they wish to use the itxalign feature other than its default mode, they can do so in the base.cfg or their configuration file.
Other information:
Updated read.me so it is more readable. Reordered paragraphs, paraphrased sentences, and added clarifications. (I will update Tracks & Markers section in the next update.)