rabhit (version 0.2.5)

deletionHeatmap: Graphical output of single chromosome deletions

Description

The deletionHeatmap function generates a graphical output of the single chromosome deletions in multiple samples.

Usage

deletionHeatmap(
  hap_table,
  chain = c("IGH", "IGK", "IGL", "TRB", "TRA"),
  kThreshDel = 3,
  genes_order = NULL,
  html_output = FALSE
)

Value

A single chromosome deletion visualization.

Arguments

hap_table

haplotype summary table. See details.

chain

the IG chain: IGH,IGK,IGL. Default is IGH.

kThreshDel

the minimum lK (log10 of the Bayes factor) used in createFullHaplotype to call a deletion. Indicates the color for strong deletion. Default is 3.

genes_order

A vector of the genes by the desired order. Default is by GENE.loc

html_output

If TRUE, a html5 interactive graph is outputed insteaed of the normal plot. Default is FALSE

Details

A data.frame created by createFullHaplotype.

Examples

# Plotting single choromosme deletion from haplotype inference
deletionHeatmap(samplesHaplotype)