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subcommand = args.subcommand_name
if subcommand == "replot":
# reproduce plots using GSEAPY
from .gsea import Replot
rep = Replot(indir=args.indir, outdir=args.outdir, weighted_score_type=args.weight,
figsize=args.figsize, graph_num=args.graph,
format=args.format, verbose=args.verbose)
rep.run()
elif subcommand == "gsea":
# compute using GSEAPY
from .gsea import GSEA
gs = GSEA(args.data, args.gmt, args.cls, args.outdir,
args.mins, args.maxs, args.n, args.weight,
args.type, args.method, args.ascending, args.threads,
args.figsize, args.format, args.graph, args.noplot, args.seed, args.verbose)
gs.run()
elif subcommand == "prerank":
from .gsea import Prerank
pre = Prerank(args.rnk, args.gmt, args.outdir, args.label[0], args.label[1],
args.mins, args.maxs, args.n, args.weight, args.ascending, args.threads,
args.figsize, args.format, args.graph, args.noplot, args.seed, args.verbose)
pre.run()
elif subcommand == "ssgsea":
from .gsea import SingleSampleGSEA
ss = SingleSampleGSEA(data=args.data, gene_sets=args.gmt, outdir=args.outdir,
sample_norm_method=args.norm,
:return: Return a GSEA obj. All results store to a dictionary, obj.results,
where contains::
| {es: enrichment score,
| nes: normalized enrichment score,
| p: P-value,
| fdr: FDR,
| size: gene set size,
| matched_size: genes matched to the data,
| genes: gene names from the data set
| ledge_genes: leading edge genes}
"""
gs = GSEA(data, gene_sets, cls, outdir, min_size, max_size, permutation_num,
weighted_score_type, permutation_type, method, ascending, processes,
figsize, format, graph_num, no_plot, seed, verbose)
gs.run()
return gs