ggbox: A box or violin plot with significance test

Description Usage Arguments Value Author(s) Examples

Description

A box or violin plot with significance test

Usage

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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

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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.