mp_plot_diff_res-methods: The visualization of result of mp_diff_analysis

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

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.

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.