mp_plot_diff_res {MicrobiotaProcess}R Documentation

The visualization of result of mp_diff_analysis

Description

The visualization of result of mp_diff_analysis

Usage

mp_plot_diff_res(
  .data,
  layout = "radial",
  tree.type = "taxatree",
  .taxa.class = NULL,
  tiplab.size = 2,
  offset.abun = 0.04,
  pwidth.abun = 0.8,
  offset.effsize = 0.3,
  pwidth.effsize = 0.5,
  group.abun = FALSE,
  tiplab.linetype = 3,
  ...
)

## S4 method for signature 'MPSE'
mp_plot_diff_res(
  .data,
  layout = "radial",
  tree.type = "taxatree",
  .taxa.class = NULL,
  tiplab.size = 2,
  offset.abun = 0.04,
  pwidth.abun = 0.8,
  offset.effsize = 0.3,
  pwidth.effsize = 0.5,
  group.abun = FALSE,
  tiplab.linetype = 3,
  ...
)

## S4 method for signature 'tbl_mpse'
mp_plot_diff_res(
  .data,
  layout = "radial",
  tree.type = "taxatree",
  .taxa.class = NULL,
  tiplab.size = 2,
  offset.abun = 0.04,
  pwidth.abun = 0.8,
  offset.effsize = 0.3,
  pwidth.effsize = 0.5,
  group.abun = FALSE,
  tiplab.linetype = 3,
  ...
)

## S4 method for signature 'grouped_df_mpse'
mp_plot_diff_res(
  .data,
  layout = "radial",
  tree.type = "taxatree",
  .taxa.class = NULL,
  tiplab.size = 2,
  offset.abun = 0.04,
  pwidth.abun = 0.8,
  offset.effsize = 0.3,
  pwidth.effsize = 0.5,
  group.abun = FALSE,
  tiplab.linetype = 3,
  ...
)

Arguments

.data

MPSE or tbl_mpse after run mp_diff_analysis with action="add"

layout

the type of tree layout, should be one of "rectangular", "roundrect", "ellipse", "circular", "slanted", "radial", "inward_circular".

tree.type

one of 'taxatree' and 'otutree', taxatree is the taxonomy class tree 'otutree' is the phylogenetic tree built with the representative sequences.

.taxa.class

character the name of taxonomy class level, default is NULL, meaning it will extract the phylum annotation automatically.

tiplab.size

numeric the size of tiplab, default is 2.

offset.abun

numeric the gap (width) (relative width to tree) between the tree and abundance panel, default is 0.04.

pwidth.abun

numeric the panel width (relative width to tree) of abundance panel, default is 0.3 .

offset.effsize

numeric the gap (width) (relative width to tree) between the tree and effect size panel, default is 0.3 .

pwidth.effsize

numeric the panel width (relative width to tree) of effect size panel, default is 0.5 .

group.abun

logical whether to display the relative abundance of group instead of sample, default is FALSE.

tiplab.linetype

numeric the type of line for adding line if 'tree.type' is 'otutree', default is 3 .

...

additional parameters, meaningless now.


[Package MicrobiotaProcess version 1.6.6 Index]