heatMapPAM: An expansion of ggtree's gheatmap function for displaying an...

In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes

An expansion of ggtree's gheatmap function for displaying an allelic presence-absence matrix.

Description

To append a heatmap of a presence-absence matrix (PAM) to the right side of a phylogenetic tree. This function is modified from the function gheatmap in the R package ggtree (github.com/GuangchuangYu/ggtree) through replacing scale_fill_gradient with scale_fill_discrete. As a result, columns in the heat map can be coloured by group information. This function is useful when users need draw a heat map of gene or allele contents across strains.

For each entry in the PAM, this function assumes that the absence status is coded as zero and the presence status is coded as one.

Usage

heatMapPAM(
  p,
  data,
  col_colours = "black",
  null_colour = "grey90",
  presence_label = "Presence",
  absence_label = "Absence",
  border_colour = "white",
  cluster_cols = FALSE,
  cluster_method = "single",
  cluster_distance = "binary",
  rev_cols = FALSE,
  colnames = TRUE,
  colnames_position = "bottom",
  colnames_angle = 0,
  colnames_level = NULL,
  set_label_colours = FALSE,
  colnames_offset_x = 0,
  colnames_offset_y = 0,
  font.size = 4,
  hjust = 0.5,
  offset = 0,
  width = 1,
  show_legend = FALSE
)

Arguments

p	A tree view from the function ggtree in the package ggtree
data	A binary presence-absence matrix (PAM)
col_colours	Either a vector of colour codes named by column names of the PAM, or a single colour code (for example, "red") for presence status in all columns.
null_colour	The colour for absence status.
presence_label	The label for presence status in the legend. Default: Presence. This parameter only works when col_colours equals a single colour code.
absence_label	The label for absence status in the legend. Default: Absence. This parameter also only works when col_colours equals a single colour code.
border_colour	Colour of heatmap cell border
cluster_cols	A logical argument determining if columns of PAM will be clustered or not. Default: FALSE. Clustering will not run when there are less than three columns in the PAM.
cluster_method	Method for clustering. Default: binary.
cluster_distance	The distance used for clustering columns. Default: binary.
rev_cols	A logical argument specifying whether to reverse the column order when it is necessary for a better visualisation.
colnames	Logical, add matrix colnames or not
colnames_position	One of 'bottom' or 'top'
colnames_angle	Angle of column names
colnames_level	Levels of colnames
set_label_colours	Whether colour column names in the same way as painting columns. By default, this option is turned off, which result in all column names to be printed in black.
colnames_offset_x	x offset for column names
colnames_offset_y	y offset for column names
font.size	Font size of matrix colnames
hjust	hjust for column names (0: align left, 0.5: align center, 1: align righ)
offset	Offset of heatmap to tree
width	Total width of heatmap, compare to width of tree
show_legend	A logical argument determining whether to show the legend.

Value

A list of three elements: p, a tree view that can be plotted directly; mapping: a data frame mapping allele names to colours; data, a data frame of weighted presence-absence status.

Author(s)

Guangchuang Yu, Yu Wan ([e-mail])

Examples

htmap <- heatMapPAM(...)
plot(htmap$p)

wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.