plotLDmatrix: LocusExplorer - LD plot matrix heatmap

In oncogenetics/oncofunco: Custom function for Oncogenetics team

LocusExplorer - LD plot matrix heatmap

Description

LD plot for LocusExplorer.

Usage

plotLDmatrix(
  data = NULL,
  xStart = NULL,
  xEnd = NULL,
  hits = NULL,
  hitsName = hits,
  hitsLabel = TRUE,
  hitsNameLength = 20,
  cols = c("lightblue", "#fef0d9", "#fdcc8a", "#fc8d59", "#e34a33", "#b30000"),
  title = NULL,
  legend = TRUE
)

Arguments

data	plink LD output format, data.frame object with c("BP_A","SNP_A","BP_B","SNP_B","R2") columns.
xStart, xEnd	Region range, zoom, minimum BP and maximum BP, advised to keep this less than 5Mb.
hits	SNP names to label in the plot. Must be present in assoc data.frame.
hitsName	Alternative SNP names to label in the plot. Default same as 'hits'
hitsLabel	Default is TRUE, set to FALSE not to show SNP names on the plot.
hitsNameLength	Maximum characters for the label.
cols	colours, length 6.
title	Character string for plot title. Default is NULL, i.e.: no plot title.
legend	Show plot legend, default TRUE.

Value

a ggplot object

Author(s)

Tokhir Dadaev

oncogenetics/oncofunco documentation built on March 9, 2024, 5:23 p.m.