mosasicPlot: Visualization of overall bins data

In GOVS-pack/GOVS: Genome optimization via virtual simulation

Visualization of overall bins data

Description

Mosasic plot for overall bins data

Usage

mosaicPlot(bins,binsInfo,chr,resolution = 500,list,parentNum = 24,color,
           clust = T,methods = "ward.D2",
           dist_method = "euclidean")

Arguments

bins	Results of IBD analysis (bins matrix), each row represents a bin fragment as well as each column represents each sample.
binsInfo	Data frame, including bins index, start, end, length of bins locus.
chr	Which chromesome will be used to plot mosaic.
resolution	To set the resolution of mosaic plot, default 500.
list	The names of lines to visualize mosaic plot.
parentNum	The number of parent, if color not defined, this parameter is used to auto generate color palette.
color	A array to define color palette.
clust	Boolean values determining if lines should be hclust object.
methods	Clustering method used. Accepts the same values as hclust.
dist_method	The distance measure to be used for clustering. See dist

Author(s)

Qian Cheng, Shuqin Jiang, Xiangfeng Wang

See Also

bins

Examples

## load data
data(bins)
data(binsInfo)
## color
color <- c("#DA053F","#FC0393","#C50F84","#D870D4","#DCA0DC","#4A0380",
            "#9271D9","#0414FB","#2792FC","#4883B2","#2CFFFE","#138B8A",
            "#42B373","#9BFB9C","#84FF2F","#566B32","#FED62D","#FD8A21",
            "#F87E75","#B01D26","#7E0006","#A9A9A9","#FFFE34","#FEBFCB")

mosaicPlot(bins = bins,binsInfo = binsInfo,chr = 1,resolution = 500,
                  color = color,
                  list = colnames(bins)[1:200])

GOVS-pack/GOVS documentation built on Oct. 9, 2022, 8:29 a.m.