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

Description Usage Arguments Details Value Author(s) References Examples

View source: R/Plot.deg.R

Description

Plot the binary differential expression matrix transformed by bi.deg

Usage

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

Arguments

input

a 'deg' object returned by bi.deg

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

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## 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.