Multiqc: Change bowtie1 color plot

[nservant]

Hi,

I tried to change the bowtie1 color code following the explanation from the doc.

custom_plot_config:
  bowtie1_alignment:
    reads_aligned:
      color: '#d84e2f'
    multimapped:
      color: '#f2e63f'
    not_aligned:
      color: '#8bbc21'

I'm sure about the plot name. Look at the bowtie1 code to find the key name ...
No error message ... Just that nothing changes.
Thanks
Nicolas

[nservant]

Actually, even the example in the doc does not seem to work for me ...

custom_plot_config:
    fastqc_sequence_counts_plot:
        cpswitch_c_active: False

[nservant]

Sorry my fault. The examples from the doc works well with the MultiQC 1.7 version.
However, my bowtie1 stuff still does not work

[nservant]

For trace, I tried to do the same with RSeQC ... no change ...

custom_plot_config:
   rseqc_read_distribution_plot:
     scale: 'Set3'

However, I'm not sure here that scale is the good key to change these colors ...

[nservant]

Actually, it seems that only keys which are accessible through pconfig can be updated.
@ewels, could you please confirm ?

[ewels]

Actually, it seems that only keys which are accessible through pconfig can be updated.

Yes - that's what this config option does, it just overwrites the pconfig supplied by the module..

[nservant]

So do you think there is a way to have access to the cats in the barplot functions ? Thks

[ewels]

If you pull the latest development version, yes 😀 I just added support for this..

[nservant]

Thanks Phil. I wlll try

[ewels]

Great! Let me know how you get on..

[nservant]

@ewels , the code that I put at the top of the issue was correct ?
Because, I have an error with the last devel version

============================================================
Module bowtie1 raised an exception: Traceback (most recent call last):
  File "/data/users/nservant/Apps/conda/multiqc/bin/multiqc", line 448, in multiqc
    output = mod()
  File "/data/users/nservant/Apps/conda/multiqc/lib/python3.6/site-packages/multiqc/modules/bowtie1/bowtie1.py", line 48, in __init__
    self.bowtie_alignment_plot()
  File "/data/users/nservant/Apps/conda/multiqc/lib/python3.6/site-packages/multiqc/modules/bowtie1/bowtie1.py", line 141, in bowtie_alignment_plot
    plot = bargraph.plot(self.bowtie_data, keys, config)
  File "/data/users/nservant/Apps/conda/multiqc/lib/python3.6/site-packages/multiqc/plots/bargraph.py", line 127, in plot
    for kk, vv in v.items():
AttributeError: 'list' object has no attribute 'items'
============================================================

[nservant]

ok. It works ! I put a list before. Thanks