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zhoulab / sclc-scripts

scripts for "Significantly mutated genes and regulatory pathways in SCLC—a meta-analysis"
https://doi.org/10.1016/j.cancergen.2017.05.003
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co-mut plot for p < 0.05 genes #9

Closed varsh1090 closed 7 years ago

varsh1090 commented 7 years ago

Command used -

python genes_001.py --mutsig_genes_file ../data/SigGenes_005.txt --mutation_tsv_file ../data/4dataset_nonsilent.txt -p 0.05 -o ../results/SCLC_comut_plot_005.pdf --sample_id_out ../results/SampleIDs005.txt --num_genes 225

The figure does not seem right, I am not sure what is the issue, could be because the dimensions dont fit 225 genes in the list. Please take a look and let me know how to fix this. Thanks

victorlin commented 7 years ago

The plot was not designed to fit --num_genes 225. We used it with the top 10 genes in the past. If you want more genes, I could increase the vertical height of the plot, or we would have to discuss how to arrange them visually so the plot is readable.

varsh1090 commented 7 years ago

Dr. Zhou wants the plot for the 225 genes to be in the supplementary data, even if it is not that readable. If we could observe the patterns of mutations and gene names, that would suffice. Please let me know if you could modify the height of the plot and we can see how it looks.

victorlin commented 7 years ago

sclc_comut_plot_005

SCLC_comut_plot_005.pdf

varsh1090 commented 7 years ago

Thanks, could we also have a comut plot for the p<0.01 genes? These are much less in number (--num_genes 56).

varsh1090 commented 7 years ago

Do we have that plotted already from before? I feel like we did but I cant find it in HPC.

victorlin commented 7 years ago

Here is the result with --num_genes 56:

sclc_comut_plot_005

SCLC_comut_plot_005.pdf

Basically you have to change the fontsize in this line:

ax1.set_yticklabels(genes_list, fontsize=13, va='center', minor=True)

and adjust the dimensions in this line:

plt.rcParams["figure.figsize"] = [20.0, 5.0]

I've also removed the legend from these renderings for simplicity.

varsh1090 commented 7 years ago

Great, thanks. This file should be renamed to SCLC_comut_plot_0.01.pdf

victorlin commented 7 years ago

Uploaded everything to /ufrc/zhou/share/projects/bioinformatics/SCLC/sclc-scripts/results/comutation-plot_031217.

varsh1090 commented 7 years ago

Thanks, this issue can be closed.