network_plots_gephi.py

Create network plots based on correlation matrix.

usage: network_plots_gephi.py [-h] [-go GEXF_OUT] [-fp FIL_PCT] [-w STATS_OUT_FNH] biom_file mapping_file condition_column in_corr_mat cat_name

Required Arguments

biom_file

The biom-format file.

mapping_file

Mapping file for reading sampleIDs and their groups.

condition_column

Column name in mapping file denoting the categories.

in_corr_mat

Correlation matrix file. The format for the tab-separated file should be: Category -> Variable -> by Variable -> Correlation

cat_name

Category to be plotted.

Optional Arguments

-go GEXF_OUT, --gexf_out GEXF_OUT

The directory to output the PCoA plots to.

--scaling_factor SCALING_FACTOR

Graph information written to this Graph Exchange XML Format file. This file can be input to Gephi.

-fp FIL_PCT, --fil_pct FIL_PCT

Specify the minimum value of correlation strength to display. By default, all correlations greater than or equal to 0.75 will be shown.

-w STATS_OUT_FNH, --stats_out_fnh STATS_OUT_FNH

Write out graph statistics - degree and betweenness centrality calculations for each node.

-h, --help

Show this help message and exit