ggdiffbox: boxplot for the result of diff_analysis

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

boxplot for the result of diff_analysis

Description

boxplot for the result of diff_analysis

Usage

ggdiffbox(obj, ...)

## S4 method for signature 'diffAnalysisClass'
ggdiffbox(
  obj,
  geom = "boxplot",
  box_notch = TRUE,
  box_width = 0.05,
  dodge_width = 0.6,
  addLDA = TRUE,
  factorLevels = NULL,
  featurelist = NULL,
  removeUnknown = TRUE,
  colorlist = NULL,
  l_xlabtext = NULL,
  ...
)

Arguments

obj	object, diffAnalysisClass class.
...	additional arguments.
geom	character, "boxplot" or "violin", default is "boxplot".
box_notch	logical, see also 'notch' of geom_boxplot, default is TRUE.
box_width	numeric, the width of boxplot, default is 0.05
dodge_width	numeric, the width of dodge of boxplot, default is 0.6.
addLDA	logical, whether add the plot to visulize the result of LDA, default is TRUE.
factorLevels	list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.
featurelist	vector, the character vector, the sub feature of originalD in diffAnalysisClass,default is NULL.
removeUnknown	logical, whether remove the unknown taxonomy, default is TRUE.
colorlist	character, the color vector, default is NULL.
l_xlabtext	character, the x axis text of left panel, default is NULL.

Value

a 'ggplot' plot object, a box or violine plot for the result of diffAnalysisClass.

Author(s)

Shuangbin Xu

Examples

## Not run: 
data(kostic2012crc)
kostic2012crc %<>% as.phyloseq()
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)
p <- ggdiffbox(diffres, box_notch=FALSE, l_xlabtext="relative abundance")
# set factor levels
p2 <- ggdiffbox(diffres, box_notch=FALSE, l_xlabtext="relative abundance", 
                factorLevels=list(DIAGNOSIS=c("Tumor", "Healthy")))

## End(Not run)

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