plotAdmixture: Admixture Plots

Description Usage Arguments Details Value

View source: R/plotAdmixture.R

Description

Generate admixture graphs for NetView or plot admixture proportions with Structure Plot.

Usage

1
plotAdmixture(qFile="oyster.4.Q", metaData=oysterData, graph=NULL, palette="Dark2", colourN=8, structurePlot=TRUE, save=FALSE)

Arguments

qFile

Output file for ancestry proportions from Admixture (.Q)

metaData

Data frame with meta data as for NetView; required columns 'ID', 'Group' and 'Colour'

graph

Network object iGraph for generating Admixture Graph [ graph, NULL ]

options

NetView options for specification of columns in metaData [ netviewOptions() ]

palette

Colour palette from RColorBrewer or vector of colours (length K) [ str, "Dark2" ]

colourN

Number of colours to include in palette, see RColorBrewer [ int, 8 ]

structurePlot

Generate admixture proportion bar plot using Structure Plot [ bool, TRUE ]

save

Name of to save ancestry file in working directory with column ID for input to Cytoscape [ str, NULL ]

Details

For examples and tutorials, please see our GitHub Repository: https://github.com/esteinig/netview

Value

Graph object with data for plotting admixture proportions or bar plot from Structure Plot.


esteinig/netview documentation built on Feb. 8, 2022, 7:17 a.m.