ggbox: A box or violin plot with significance test

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

Description

A box or violin plot with significance test

Usage

ggbox(obj, factorNames, ...)

## S4 method for signature 'data.frame'
ggbox(
  obj,
  sampleda,
  factorNames,
  indexNames,
  geom = "boxplot",
  factorLevels = NULL,
  compare = TRUE,
  testmethod = "wilcox.test",
  signifmap = FALSE,
  p_textsize = 2,
  step_increase = 0.1,
  boxwidth = 0.2,
  facetnrow = 1,
  controlgroup = NULL,
  comparelist = NULL,
  ...
)

## S4 method for signature 'alphasample'
ggbox(obj, factorNames, ...)

Arguments

obj	object, alphasample or data.frame (row sample x column features).
factorNames	character, the names of factor contained in sampleda.
...	additional arguments, see also stat_signif.
sampleda	data.frame, sample information if obj is data.frame, the sampleda should be provided.
indexNames	character, the vector character, should be the names of features contained object.
geom	character, "boxplot" or "violin", default is "boxplot".
factorLevels	list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.
compare	logical, whether test the features among groups,default is TRUE.
testmethod	character, the method of test, default is 'wilcox.test'. see also stat_signif.
signifmap	logical, whether the pvalue are directly written a annotaion or asterisks are used instead, default is (pvalue) FALSE. see also stat_signif.
p_textsize	numeric, the size of text of pvalue or asterisks, default is 2.
step_increase	numeric, see also stat_signif, default is 0.1.
boxwidth	numeric, the width of boxplot when the geom is 'violin', default is 0.2.
facetnrow	integer, the nrow of facet, default is 1.
controlgroup	character, the names of control group, if it was set, the other groups will compare to it, default is NULL.
comparelist	list, the list of vector, default is NULL.

Value

a 'ggplot' plot object, a box or violine plot.

Author(s)

Shuangbin Xu

Examples

library(magrittr)
otudafile <- system.file("extdata", "otu_tax_table.txt",
                         package="MicrobiotaProcess")
otuda <- read.table(otudafile, sep="\t", 
                    header=TRUE, row.names=1,
                    check.names=FALSE, skip=1, 
                    comment.char="")
samplefile <- system.file("extdata",
                          "sample_info.txt", 
                          package="MicrobiotaProcess")
sampleda <- read.table(samplefile,
                       sep="\t", header=TRUE, row.names=1)
otuda <- otuda[sapply(otuda, is.numeric)] %>% t() %>%
         data.frame(check.names=FALSE)
set.seed(1024)
alphaobj1 <- get_alphaindex(otuda, sampleda=sampleda)
p1 <- ggbox(alphaobj1, factorNames="group")
data(test_otu_data)
set.seed(1024)
alphaobj2 <- get_alphaindex(test_otu_data)
class(alphaobj2)
head(as.data.frame(alphaobj2))
p2 <- ggbox(alphaobj2, factorNames="group")
# set factor levels.
#p3 <- ggbox(obj=alphaobj2, factorNames="group", 
#            factorLevels=list(group=c("M", "N", "B", "D")))
# set control group.
#p4 <- ggbox(obj=alphaobj2, factorNames="group", controlgroup="B")
# set comparelist
#p5 <- ggbox(obj=alphaobj2, factorNames="group", 
#            comparelist=list(c("B", "D"), c("B", "M"), c("B", "N")))

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