ggdiffbox {MicrobiotaProcess} | R Documentation

## 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
    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)

[Package MicrobiotaProcess version 1.4.4 Index]