Plot.deg.specific.test: Plot the DEGs before or after cross-validation

In menggf/decd: A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

Description

Plot the cross-validated DEGs predicted by deg.specific.

Usage

## S3 method for class 'deg.specific.test'
Plot(input, ann = NULL, col.order = NULL,
  show.genes = NULL, max.n = 30, up.col = "#008000",
  down.col = "#CD5B45")

Arguments

input	a 'deg.specific' object returned by deg.specific
ann	a data.frame for the patient annotation
col.order	the order of column in heatmap
show.genes	the gene ids to plot
max.n	the maximum number of genes to plot
up.col	the color for up-regulated genes
down.col	the color for down-regulated genes

Details

This function applied the function of oncoPrint from 'ComplexHeatmap' to dispaly ownership of the DEGs. The output is a heatmap plots where the genes with maximum observations are showed.

Value

A heatmap plot

Author(s)

Guofeng Meng

References

Gu Z, Eils R and Schlesner M (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics.

Examples

## Not run: 
Plot(deg,er.ann, max.n=15)
Plot(res.deg, er.ann, max.n=15)
Plot(res.deg, ann=er.ann, show.genes=c("ESR1","FOXA1","GATA3"))
Plot(res.deg, ann=er.ann, up.col="#008000", down.col="#CD5B45")

## End(Not run)

menggf/decd documentation built on Jan. 2, 2020, 12:53 a.m.