plot_heatmap {microbiomeMarker} | R Documentation |
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, ... )
mm |
a |
transform |
transformation to apply, for more details see
|
cluster_marker, cluster_sample |
logical, controls whether to perform
clustering in markers (rows) and samples (cols), default |
markers |
character vector, markers to display, default |
label_level |
integer, number of label levels to be displayed, default
|
max_label_len |
integer, maximum number of characters of feature label,
default |
sample_label |
logical, controls whether to show the sample labels in
the heatmap, default |
scale_by_row |
logical, controls whether to scale the heatmap by the
row (marker) values, default |
annotation_col |
assign colors for the top annotation using a named
vector, passed to |
group |
character, the variable to set the group |
... |
extra arguments passed to |
a ComplexHeatmap::Heatmap
object.
transform_abundances
,ComplexHeatmap::Heatmap()
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")