plot_overlapping: Plot overlapping between data and grouping factors

In GALLO: Genomic Annotation in Livestock for Positional Candidate LOci

Plot overlapping between data and grouping factors

Description

Takes the output from overlapping_among_groups function and creates a heatmap with the overlapping between groups

Usage

plot_overlapping(overlapping_matrix, nmatrix, ntext, group, labelcex = 1)

Arguments

overlapping_matrix	The object obtained in overlapping_amoung_groups function
nmatrix	An interger from 1 to 3 indicating which matrix will be used to plot the overlapping, where: 1) A matrix with the number of overllaping data; 2) A matrix with the percentage of overlapping; 3) A matrix with the combination of the two previous one
ntext	An interger from 1 to 3 indicating which matrix will be used as the text matrix for the heatmap, where: 1) A matrix with the number of overllaping data; 2) A matrix with the percentage of overlapping; 3) A matrix with the combination of the two previous one
group	A vector with the size of groups. This vector will be plotted as row and column names in the heatmap
labelcex	A numeric value indicating the size of the row and column labels

Value

A heatmap with the overlapping between groups

Examples

data(QTLmarkers)
data(gtfGenes)
genes.out <- find_genes_qtls_around_markers(
db_file=gtfGenes, marker_file=QTLmarkers,
method="gene", marker="snp",interval=100000,
nThreads=1)

overlapping.out<-overlapping_among_groups(
file=genes.out,x="Reference",y="gene_id")
plot_overlapping(overlapping.out,
nmatrix=2,ntext=2,
group=unique(genes.out$Reference))

GALLO documentation built on June 22, 2024, 9:17 a.m.