mp_plot_diff_res-methods: The visualization of result of mp_diff_analysis

mp_plot_diff_resR Documentation

The visualization of result of mp_diff_analysis

Description

The visualization of result of mp_diff_analysis

Usage

mp_plot_diff_res(
  .data,
  .group,
  layout = "radial",
  tree.type = "taxatree",
  .taxa.class = NULL,
  barplot.x = NULL,
  point.size = NULL,
  sample.num = 50,
  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,
  .group,
  layout = "radial",
  tree.type = "taxatree",
  .taxa.class = NULL,
  barplot.x = NULL,
  point.size = NULL,
  sample.num = 50,
  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,
  .group,
  layout = "radial",
  tree.type = "taxatree",
  .taxa.class = NULL,
  barplot.x = NULL,
  point.size = NULL,
  sample.num = 50,
  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,
  .group,
  layout = "radial",
  tree.type = "taxatree",
  .taxa.class = NULL,
  barplot.x = NULL,
  point.size = NULL,
  sample.num = 50,
  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"

.group

the column name for mapping the different color, default is the column name has 'Sign_' prefix, which contains the enriched group name, but the insignificant should be NA.

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.

barplot.x

the column name of continuous value mapped to barplot, default is NULL, meaning the 'LDAmean' will be used internally.

point.size

the column name of continuous value mapped to the size of point in the tree, default is NULL, meaning the 'fdr' will be used internally.

sample.num

integer when it is smaller than the sample number of '.data', the abundance of '.group' will replace the abundance of sample, default is 50.

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.


xiangpin/MicrobiotaProcess documentation built on July 24, 2024, 11:44 p.m.