Added directory and code to examples\ to reproduce Figure 2 with S.c and S.p
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mdml
requested changes
Mar 26, 2018
example/dissim-plot/plot_kde.py
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| plt.ylabel('Density', size = font_size) | ||
| plt.xlabel(xlabel, size = font_size) | ||
| plt.legend(loc='best', fontsize = font_size) | ||
| plt.savefig(output) |
example/dissim-plot/plot_kde.py
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| def plot_and_save(scores_and_labels, xlabel, output, | ||
| xmin=0.0, | ||
| xmax=0.6, |
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Should the xmax provided in the config file? Or is this usually the same across species pairs?
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xmax can be provided in the config file, 0.6 is just a value I picked as the default
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xmax can be provided via the configuration file. There is no obvious way to figure out what xmax should be a priori, so I just picked a default.
example/dissim-plot/plot_kde.py
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| plot_and_save(plots, 'Dissimilarity scores', args.output) | ||
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| # Load |
mdml
approved these changes
Apr 2, 2018
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Homologs are more similar in HANDL space than non-homologs
In this example, we show that HANDL scores are correlated with functional similarity by reproducing Figure 2a and Figure 2b (as well as Figure S1 and S2 in the S.I).
Usage
To produce Figure 2 from [REF] simply execute
snakemake all --configfile configs/<configfile>Provided configuration files:
We provide example configuration files for the following:
configs/sc-sp.ymlis a configuration file to produce plots of HANDL dissimilarity scores between S.c and S.p proteins projected into HANDL space with S.c as the source and S.p as the target, respectively. PPI networks from which HANDL scores and embeddings are computed can be found in thedatadirectory in the root folder and are obtained from BioGrid v3.4.157.configs/human-sc.yml,configs/human-mouse.yml,configs/mouse-sc.yml, are a configuration files to produce plots of HANDL dissimilarity scores between homolog pairs and other pairs and plots of HANDL vs Resnik scores.Data
snakemakein/datain the root directory to download PPI networks and Resnik scores required to produce plots. (Note that Resnik scores are precomputed and downloaded directly from the UMIACS Object Store.)