plot.MH: Visualize mountain-hill landscape with package 'rgl'

In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description

Visualizing gene mutation as mountain-hill landscape, containing mountain genes and hill genes.

Usage

plot.MH(df, refgene, label.genes=NA, k=400, xmin=4, xmax=300, ymin=4, ymax=268, magnitude=40, shift=2, z.padj=0.5, cex=1)

Arguments

df	A data frame with 3 columns, the 1st col is gene name, 2nd mutation frequency, and 3rd q-value.
refgene	A data frame with 3 columns containing information about gene distribution across genome.
label.genes	gene(s) to be labeled in mountain-hill landscape.
k	Number of genes to visualize.
xmin	Start position in x-axis.
xmax	End position in x-axis.
ymin	Start position in y-axis.
ymax	End position in y-axis.
magnitude	Times to be magnified.
shift	Shift units along axis.
z.padj	Adjustment along z-axis.
cex=1	Text size.

Details

Use package rgl to visualize gene mutation as mountain-hill landscape.

Examples

library(rgl)
data("MH",package="lxctk")
data("refgene",package="lxctk")
plot.MH(MH, refgene, label.genes=c('APC','TP53','PIK3CA'))

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.