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