ggdiffclade: plot the clade tree with highlight

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

Description

plot results of different analysis or data.frame, contained hierarchical relationship or other classes,such like the tax_data of phyloseq.

Usage

ggdiffclade(obj, ...)

## S3 method for class 'data.frame'
ggdiffclade(
  obj,
  nodedf,
  factorName,
  layout = "circular",
  linewd = 0.6,
  skpointsize = 0.8,
  alpha = 0.4,
  taxlevel = 6,
  cladetext = 2,
  factorLevels = NULL,
  setColors = TRUE,
  xlim = 12,
  reduce = FALSE,
  type = "species",
  ...
)

## S3 method for class 'diffAnalysisClass'
ggdiffclade(obj, removeUnknown = TRUE, ...)

Arguments

obj	object, diffAnalysisClass, the results of diff_analysis see also diff_analysis, or data.frame, contained hierarchical relationship or other classes.
...,	additional parameters.
nodedf	data.frame, contained the tax and the factor information and(or pvalue).
factorName	character, the names of factor in nodedf.
layout	character, the layout of ggtree, but only "rectangular", "radial", "slanted", "inward_circular" and "circular" in here, default is circular.
linewd	numeric, the size of segment of ggtree, default is 0.6.
skpointsize	numeric, the point size of skeleton of tree, default is 0.8 .
alpha	numeric, the alpha of clade, default is 0.4.
taxlevel	positive integer, the full text of clade, default is 5.
cladetext	numeric, the size of text of clade, default is 2.
factorLevels	list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.
setColors	logical, whether set the color of clade, default is TRUE, or set FALSE,then use 'scale_fill_manual' setting.
xlim	numeric, the x limits, only works for 'inward_circular' layout, default is 12.
reduce	logical, whether remove the unassigned taxonomy, which will remove the clade of unassigned taxonomy, but the result of 'diff_analysis' should remove the unknown taxonomy, default is FALSE.
type	character, the type of datasets, default is "species", if the dataset is not about species, such as dataset of kegg function, you should set it to "others".
removeUnknown	logical, whether do not show unknown taxonomy, default is TRUE.

Value

figures of tax clade show the significant different feature.

Author(s)

Shuangbin Xu

Examples

data(kostic2012crc)
kostic2012crc
head(phyloseq::sample_data(kostic2012crc),3)
kostic2012crc <- phyloseq::rarefy_even_depth(kostic2012crc,
                         rngseed=1024)
table(phyloseq::sample_data(kostic2012crc)$DIAGNOSIS)
set.seed(1024)
diffres <- diff_analysis(kostic2012crc, classgroup="DIAGNOSIS",
                        mlfun="lda", filtermod="fdr",
                        firstcomfun = "kruskal.test",
                        firstalpha=0.05, strictmod=TRUE,
                        secondcomfun = "wilcox.test",
                        subclmin=3, subclwilc=TRUE,
                        secondalpha=0.01, ldascore=3)
#library(ggplot2)
#diffcladeplot <- ggdiffclade(diffres,alpha=0.3, linewd=0.2, 
#                        skpointsize=0.4, 
#                        taxlevel=3,
#                        setColors=FALSE) +
#        scale_fill_manual(values=c('#00AED7', 
#                                   '#FD9347', 
#                                   '#C1E168'))

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.