cirPlot4pathway: Circular plot for a set of pathways

In transbioZI/BioMMex: BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

Circular plot for a set of pathways

Description

The individual CpGs or genes within a given set of pathways are displayed as the dots in the resulting plot. The significance of the CpGs or genes are illustrated by the negative log P value.

Usage

cirPlot4pathway(datalist, topPathID, core = MulticoreParam(), fileName = NULL)

Arguments

datalist	The input data list containing ordered collections of matrices.
topPathID	A predefined pathway IDs.
core	The number of cores used for computation. (Default: 10)
fileName	Add a character to the output file name. (Default: 'Circular-Manhattan.pval.jpeg')

Details

Top 10 or 20 pathways are usually suggested to be visualized. The significant features (if any) are highlighted using filled diamond. The significance line is set as 0.05 marked as dashed red line.

Value

An output image file.

See Also

omics2pathlist.

transbioZI/BioMMex documentation built on Jan. 27, 2023, 4:14 a.m.