Heatmap of microbiome marker

Source: R/plot-heatmap.R

Display the microbiome marker using heatmap, in which rows represents the marker and columns represents the samples.

plot_heatmap(
  mm,
  transform = c("log10", "log10p", "identity"),
  cluster_marker = FALSE,
  cluster_sample = FALSE,
  markers = NULL,
  label_level = 1,
  max_label_len = 60,
  sample_label = FALSE,
  scale_by_row = FALSE,
  annotation_col = NULL,
  group,
  ...
)

Arguments

mm

a microbiomeMarker object

transform

transformation to apply, for more details see transform_abundances():

  • "identity", return the original data without any transformation.

  • "log10", the transformation is log10(object), and if the data contains zeros the transformation is log10(1 + object).

  • "log10p", the transformation is log10(1 + object).

cluster_marker, cluster_sample

logical, controls whether to perform clustering in markers (rows) and samples (cols), default FALSE.

markers

character vector, markers to display, default NULL, indicating plot all markers.

label_level

integer, number of label levels to be displayed, default 1, 0 means display the full name of the feature

max_label_len

integer, maximum number of characters of feature label, default 60

sample_label

logical, controls whether to show the sample labels in the heatmap, default FALSE.

scale_by_row

logical, controls whether to scale the heatmap by the row (marker) values, default FALSE.

annotation_col

assign colors for the top annotation using a named vector, passed to col in ComplexHeatmap::HeatmapAnnotation().

group

character, the variable to set the group

...

extra arguments passed to ComplexHeatmap::Heatmap().

Value

a ComplexHeatmap::Heatmap object.

Examples

data(kostic_crc)
kostic_crc_small <- phyloseq::subset_taxa(
    kostic_crc,
    Phylum %in% c("Firmicutes")
)
mm_lefse <- run_lefse(
    kostic_crc_small,
    wilcoxon_cutoff = 0.01,
    group = "DIAGNOSIS",
    kw_cutoff = 0.01,
    multigrp_strat = TRUE,
    lda_cutoff = 4
)
plot_heatmap(mm_lefse, group = "DIAGNOSIS")
#> Warning: OTU table contains zeroes. Using log10(1 + x) instead.