simple_heatmap: Simple Heatmap

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Simple Heatmap

Description

Create a simple heatmap with ggplot2 package.

Usage

simple_heatmap(
  x,
  group.facet = "DiseaseState",
  group.order = c("H", "CRC", "nonCRC"),
  abund.thres = 0.01,
  prev.thres = 0.1,
  level = "Genus",
  scale.color = "log10",
  na.fill = "white",
  color.fill = NULL,
  taxa.arrange = TRUE,
  panel.arrange = NULL,
  remove.other = TRUE,
  ncol = NULL,
  nrow = NULL
)

Arguments

x	phyloseq-class object.
group.facet	Variable to make facet/panel the plot.
group.order	Default is NULL. a list specifing order of x-axis. E.g. c("H","CRC","nonCRC")
abund.thres	= 0.01 check microbiome package aggregate_rare function.
prev.thres	= 0.1 check microbiome package aggregate_rare function.
level	= "Genus" Taxonomic level. OTU/ASV level not supported. Check plot_taxa_heatmap
scale.color	Scale the tiles colors "log10" or "sqrt"
na.fill	Color to fill NAs. e.g. "white"
color.fill	User specified color vectors.
taxa.arrange	Arrange the order of taxa. User can supply a list of vectors.
panel.arrange	panels "grid" or "wrap" ggplot's facet_XXX
remove.other	Rare clubbed as Other to be removed. Logical TRUE/FALSE.
ncol	if wrap, specify number of columns.
nrow	if wrap, specify number of rows.

Details

Wrapper converts phyloseq-class object to long data frame and generates a heatmap.

Value

ggplot object.

Examples

library(microbiome)
library(microbiomeutilities)
library(dplyr)
data("zackular2014")
p0 <- zackular2014
p0.rel <- transform(p0, "compositional")
p <- simple_heatmap(p0.rel,
  group.facet = "DiseaseState",
  group.order = c("H", "CRC", "nonCRC"),
  abund.thres = 0.01,
  prev.thres = 0.1,
  level = "Genus",
  scale.color = "log10",
  na.fill = "white",
  color.fill = NULL,
  taxa.arrange = TRUE,
  remove.other = TRUE,
  panel.arrange = "wrap",
  ncol = 2,
  nrow = 2
)

print(p)

microsud/microbiomeutilities documentation built on Nov. 29, 2022, 12:18 a.m.