xadmix (version 1.0.0)

admix_barplot: Admixture Data Stacked Barplot

Description

Stacked barplot optimized for admixture data.

Usage

admix_barplot(
  data,
  K = 2:ncol(data),
  individuals = 1,
  sortkey = NULL,
  grouping = NULL,
  palette = "default",
  names = TRUE,
  xlab = "Individuals",
  ylab = "Ancestry",
  main = "Admixture Plot",
  noclip = FALSE
)

Value

A ggplot object of the stacked barplot.

Arguments

data

Data frame containing the admixture data.

K

Positions of the columns containing the ancestry percentages in the provided data frame; default is second to last column.

individuals

Position of the column with the names for the x-axis; default is the first column.

sortkey

Name of the column containing ancestry percentages to sort the stacked barplot with.

grouping

Name of the column by which the stacked bars are to be grouped.

palette

Either a color palette object, or a string to use one of the predefined color palettes ("viridis", "turbo", "alternating"); default is a modified ggplot palette.

names

Whether to show the x-axis bar labels or not; default is "TRUE".

xlab

A label for the x-axis.

ylab

A label for the y-axis.

main

A main title for the plot.

noclip

Directly draw the plot, with clipping removed from elements. Then function does not return an object; default is set to "FALSE". Setting to "TRUE" may require launching a new R graphics device.

Examples

# load simulated admixture data
data("xadmixture")

# for data frame with ancestries (K) in fourth to last column,
# without showing bar labels
admix_barplot(xadmixture,
    K = 4:ncol(xadmixture),
    names = FALSE
)

# grouping data by column "country",
# and sorting each group by ancestry column "K1"
admix_barplot(xadmixture,
    K = 4:ncol(xadmixture),
    grouping = "country",
    sortkey = "K1",
    names = FALSE
)

# changing color palette to "turbo" from package 'viridis',
admix_barplot(xadmixture,
    K = 4:ncol(xadmixture),
    palette = "turbo",
    names = FALSE
)

# removing title and changing axis labels text
admix_barplot(xadmixture,
    K = 4:ncol(xadmixture),
    main = "",
    xlab = "Accessions",
    ylab = "Ancestry [%]",
    names = FALSE
)

# directly output grouped plot with clipping removed from elements
# (useful if there are groups with a low number of observations)
# create a subset of the data
xadmixture_sub <- admix_subset(xadmixture,
                              anc = c("K3", "K4"), 
                              pct = c(0.3, 0.2))
# generate a grouped & sorted stacked barplot 
# setting "noclip" to "TRUE" may require opening a new graphics device
dev.new()
admix_barplot(xadmixture_sub, 
             K = 4:ncol(xadmixture),          
             sortkey = "K5",
             grouping = "country", 
             palette = "viridis", 
             names = FALSE, 
             noclip = TRUE)
dev.off()