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Haplotype labels in TSV, visualisations ? #20
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Hi Benjamin, I think the option that you're looking for is the ordered growth plot that is implemented in the subcommand |
Thanks you for your fast reply. For instance, below is my haplotype list:
The same labels are present in the GFA file.
However, whatever I try, the output CSV or plots only show 1, 2, 3, ... labels for the haplotypes. It never shows the labels. |
You're touching a sensitive issue here.. yes the documentation is rather weak. I didn't have a chance to look at my code yet, but it could be that Also, what does the log output say if you run the tool with |
Hi, Benjamin, I have the impression the meaning of the histogram might not be what you think. The histogram does not show how many bps appear in haplotype 1, how many in haplotype 2, and so on. Each bar in the histogram represents the following:
What you would like, if I am understanding correctly, is to know "how many bps appear in haplotype 1 (eg, Sungold#0#Chr1__Sungold#0), how many bps appear in haplotype 2 (eg, Stella_v1p1#0#Chr1__Stella_v1p1#0) and so on. Is it correct? |
Thank you for your explanation. But then how did you obtain the graph which is at the bottom of the readme of this github. I may be confused, but as I understand it this is the graph growth, haplotype after haplotype, because haplotype labels are on the X axis. I wanted to reproduce this graph. In the README, you have this line:
Which generates However, this file is not used in any of the commands of the README. |
@blinard-BIOINFO thanks for pointing this out, this is indeed a bug in the documentation. The correct command should be
I'm running the example now again to see whether it produces the intended output. |
@blinard-BIOINFO you are right, the labels do not come through--this seems to be a bug. Other than that, the plot is identical to the one shown in the README |
@blinard-BIOINFO: @heringerp fixed the issue. |
Hello,
Great tool.
Is it possible to display the haplotypes labels from GFA P-lines or W-lines into the TSV outputs, as well as the HTML/PDF outputs ?
I tried with different GFA files, containing either P-lines or W-lines.
However, the output always lists the haplotypes on X axes with integers from 1 to n.
If this is not implemented, does the enumeration corresponds to the order of the lines in the GFA ? or from the haplotype.txt files ?
Thanks
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