plot_heatmap: Heatmap of microbiome marker

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

Heatmap of microbiome marker

Description

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

Usage

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.

See Also

transform_abundances,ComplexHeatmap::Heatmap()

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")

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.