mp_plot_diff_cladogram: Visualizing the result of mp_diff_analysis with cladogram.

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

Visualizing the result of mp_diff_analysis with cladogram.

Description

Visualizing the result of mp_diff_analysis with cladogram.

Usage

mp_plot_diff_cladogram(
  .data,
  .group,
  .size = "pvalue",
  taxa.class,
  removeUnknown = FALSE,
  layout = "radial",
  hilight.alpha = 0.3,
  hilight.size = 0.2,
  bg.tree.size = 0.15,
  bg.tree.color = "#bed0d1",
  bg.point.color = "#bed0d1",
  bg.point.fill = "white",
  bg.point.stroke = 0.2,
  bg.point.size = 2,
  label.size = 2.6,
  tip.annot = TRUE,
  as.tiplab = TRUE,
  ...
)

Arguments

.data	MPSE object or treedata which was from the taxatree slot after running the 'mp_diff_analysis'.
.group	the column name for mapping the different color.
.size	the column name for mapping the size of points, default is 'pvalue'.
taxa.class	the taxonomy class name will be replaced shorthand, default is the one level above ‘OTU’.
removeUnknown	logical, whether mask the unknown taxonomy information but differential species, default is FALSE.
layout	character, the layout of tree, default is 'radial', see also the 'layout' of 'ggtree'.
hilight.alpha	numeric, the transparency of high light clade, default is 0.3.
hilight.size	numeric, the margin thickness of high light clade, default is 0.2.
bg.tree.size	numeric, the line size (width) of tree, default is 0.15.
bg.tree.color	character, the line color of tree, default is '#bed0d1'.
bg.point.color	character, the color of margin of background node points of tree, default is '#bed0d1'.
bg.point.fill	character, the point fill (since point shape is 21) of background nodes of tree, default is 'white'.
bg.point.stroke	numeric, the margin thickness of point of background nodes of tree, default is 0.2 .
bg.point.size	numeric, the point size of background nodes of tree, default is 2.
label.size	numeric, the label size of differential taxa, default is 2.6.
tip.annot	logcial whether to replace the differential tip labels with shorthand, default is TRUE.
as.tiplab	logical, whether to display the differential tip labels with 'geom_tiplab' of 'ggtree', default is TRUE, if it is FALSE, it will use 'geom_text_repel' of 'ggrepel'.
...	additional parameters, meaningless now.

Details

The color scale of differential group can be designed by 'scale_fill_diff_cladogram'

Examples

## Not run: 
  data(mouse.time.mpse)
  mouse.time.mpse %<>%
    mp_rrarefy()
  mouse.time.mpse
  mouse.time.mpse %<>%
    mp_diff_analysis(.abundance=RareAbundance,
                     .group=time,
                     first.test.alpha=0.01,
                     action="add")
  #' ### visualizing the differential taxa with cladogram
  library(ggplot2)
  f <- mouse.time.mpse %>%
       mp_plot_diff_cladogram(
         label.size = 2.5,
         hilight.alpha = .3,
         bg.tree.size = .5,
         bg.point.size = 2,
         bg.point.stroke = .25
       ) +
       scale_fill_diff_cladogram(
         values = c('skyblue', 'orange')
       ) +
       scale_size_continuous(range = c(1, 4))
  f

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on July 26, 2024, 4:21 a.m.