plot_cladogram {microbiomeMarker} | R Documentation |
plot cladogram of micobiomeMaker results
plot_cladogram( mm, color, branch_size = 0.2, alpha = 0.2, node_size_scale = 1, node_size_offset = 1, clade_label_level = 4, annotation_shape = 22, annotation_shape_size = 5, group_legend_param = list(), marker_legend_param = list() )
mm |
a microbiomeMarker object |
color |
a color vector, used to highlight the clades of microbiome biomarker. The values will be matched in order (usually alphabetical) with the groups. If this is a named vector, then the colors will be matched based on the names instead. |
branch_size |
numberic, size of branch, default |
alpha |
alpha parameter for shading, default |
node_size_scale |
the parameter 'a' controlling node size:
|
node_size_offset |
the parameter 'b' controlling node size:
|
clade_label_level |
max level of taxa used to label the clade, other level of taxa will be shown on the side |
annotation_shape |
shape used for annotation, default |
annotation_shape_size |
size used for annotation shape, default |
group_legend_param, marker_legend_param |
a list specifying
extra parameters of group legend and marker legend, such as |
a ggtree object
Chenhao Li, Guangchuang Yu, Chenghao Zhu, Yang Cao
This function is modified from clada.anno
from microbiomeViz.
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_cladogram(mm_lefse, color = c("darkgreen", "red"))