im_netplot: Creates and plot an igraph network from dataframe

In korkutlab/imogimap: What the Package Does (One Line, Title Case)

Creates and plot an igraph network from dataframe

Description

Creates and plot an igraph network from dataframe

Usage

im_netplot(df, icp_gene, cohort, Immune_phenotype, cutoff, seed = 1)

Arguments

df	A dataframe as outputted by im_syng_tcga or im_syng
icp_gene	An optional character vector of immune checkpoints for color coding vertex. default is icp_gene_list
cohort	An optional character string indicating a single TCGA disease.
Immune_phenotype	a character string indicating name of an immune feature.
cutoff	A numeric indicating quantile cut-off for absolute values of synergy scores.
seed	A single value, interpreted as an integer; Default: 1 (see set.seed for details).

Details

im_netplot uses igraph to construct and plot network from synergy score data frame. Dark red (Dark blue) vertices identify over-expression (low-expression) of Immune-checkpoint genes and orange (blue) vertices identify over-expression (low-expression) of oncogenes. up-regulations (down-regulations) of the immune phenotype are depicted as red (blue) edges. Thickness of an edge is determined by the absolute value of the score, and the size of each vertex is determined by its degree. Edges with absolute values lower that the cut-off will be removed from the graph.

cutoff=0 does not remove any edges. cutoff=1 removes all edges. Default is 0.95, which keeps scores with their absolute value higher than 0.95 quantile. seed is an integer that is the starting point from which random numbers are generated in igraph. Seed value is used for the reproducibility of plot layout. different seed numbers will generate different

Value

A plotted igraph object showing network of synergistic (red) and antagonistic (blue) associations.

See Also

igraph

Examples

df <- im_syng_tcga(onco_gene = icp_gene_list[1:3], icp_gene = icp_gene_list[1:3], cohort = "acc")
im_netplot(df, Immune_phenotype = "EMTscore")

korkutlab/imogimap documentation built on March 17, 2023, 8:22 a.m.