plot cladogram of micobiomeMaker results

plot cladogram of micobiomeMaker results

plot_cladogram(
  mm,
  color,
  only_marker = FALSE,
  branch_size = 0.2,
  alpha = 0.2,
  node_size_scale = 1,
  node_size_offset = 1,
  clade_label_level = 4,
  clade_label_font_size = 4,
  annotation_shape = 22,
  annotation_shape_size = 5,
  group_legend_param = list(),
  marker_legend_param = list()
)

Arguments

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.

only_marker

logical, whether show all the features or only markers in the cladogram, default FALSE.

branch_size

numeric, size of branch, default 0.2

alpha

alpha parameter for shading, default 0.2

node_size_scale

the parameter 'a' controlling node size: node_size=a*log(relative_abundance) + b

node_size_offset

the parameter 'b' controlling node size: node_size=a*log(relative_abundance) + b

clade_label_level

max level of taxa used to label the clade, other level of taxa will be shown on the side.

clade_label_font_size

font size of the clade label, default 4.

annotation_shape

shape used for annotation, default 22

annotation_shape_size

size used for annotation shape, default 5

group_legend_param, marker_legend_param

a list specifying extra parameters of group legend and marker legend, such as direction ( the direction of the guide), nrow (the desired number of rows of legends). See ggplot2::guide_legend() for more details.

Value

a ggtree object

References

This function is modified from clada.anno from microbiomeViz.

See also

ggtree::ggtree()

Author

Chenhao Li, Guangchuang Yu, Chenghao Zhu, Yang Cao

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_cladogram(mm_lefse, color = c("darkgreen", "red"))