Simple Heatmap

Create a simple heatmap with ggplot2 package.

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.

Value

ggplot object.

Details

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

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
)
#> An additonal column Sam_rep with sample names is created for reference purpose

print(p)
#> Warning: Transformation introduced infinite values in discrete y-axis