unable to set x axis of custom linegraph using tsv file

[anoronh4]

Description of unexpected behavior:
In custom content we are able to add data from several file types (json, tsv, yaml). I am attempting to add data of several samples using tsv and i am seemingly successful with the following:

SampleA	700650	7969	4991
SampleB	683285	7357	4688
SampleC	674329	7412	4632

and my config file says:

custom_data:
    customtab:
        file_format: 'tsv'
        section_name: 'Custom Data'
        plot_type: 'linegraph'
        pconfig:
            id: 'custom_linegraph'
            title: 'Custom Data Linegraph'
sp:
    customtab:
        fn: 'testfile.tsv'

Multiqc infers that the x-axis for each datapoint is 1, 2, 3 . However in my case it should be 0,1,2. But using a multi-sample tsv file, it is not obvious how i'm supposed to add that information. I tried a header line where the first field is blank, but it is treated as another row in the table and is visualized as Series0 on the linegraph (json file says{"name":"","data": [[1,0.0],[2,1.0],[3,2.0]]}). This is the table from that test:

	0	1	2
SampleA	700650	7969	4991
SampleB	683285	7357	4688
SampleC	674329	7412	4632

The only way to customize the x-axis that I can see is to use another file format like json or yaml, but this is an unexpected limitation, since tsv files are the most common and readily available input type.

File that triggers the unexpected behavior:
testfiles.zip

MultiQC run details:

• Command used to run MultiQC: multiqc .
• MultiQC Version: MultiQC v1.9
• Operating System: linux
• Python Version: Python 3.8.1
• Method of MultiQC installation: singularity container from docker://ewels/multiqc

[anoronh4]

update: i seem to be having a different but may not unrelated problem with *_mqc.json files.
demo.zip

Once again multiqc seems to be ignoring the x-labels that are entered into the custom content files, just like when i was using tsv. Strangely, the peaks in the plot are spaced in intervals of eleven.

i think the linegraph plot is maybe expecting non-string keys, but i can't manage that in json format. even the linegraph from your example here does not show the expected x-axis labeling when i run multiqc on it.

any guidance at this point would be appreciated.

[anoronh4]

update: yaml format gets better results for using the intended x-axis label, guessing because we have the liberty to use string/int keys in the data section. i'll leave this issue up because i still believe it to be a bug/area for improvement.

[zxl124]

I have run into the same thing. Basically the X-axis values are meaningless when using custom-content module to make line graphs, in JSON format. The example code in MultiQC documentation has the X-axis values in 1,2,3,4,5

"data": {
    "sample_1": { "1": 12, "2": 14, "3": 10, "4": 7, "5": 16 },
    "sample_2": { "1": 9, "2": 11, "3": 15, "4": 18, "5": 21 }
  }

but the plot comes out with X-axis values in 0,1,2,3,4

I've tried changing the X-axis values to other numbers, but the plot remained the same. I suspect converting the keys to float before feeding into HighCharts might fix this bug.

[ewels]

Hi both,

Apologies for my slow response here. I was able to reproduce your error, funny how I had never noticed this in my own docs examples 🤦🏻

Line graphs and scatter graphs no attempt to make the axis labels into floats if they can, which seems to solve that part of the problem.

Phil

[ewels]

Ok, and second part also done. I've added some logic so that if the first sample has no sample name, then the values are used for x-axis labels.

This means that your original example with the TSV file now works as you expect 👍🏻

Thanks for pointing this out and suggesting it!

Phil