ggeffectsize {MicrobiotaProcess} | R Documentation

## visualization of effect size by the Linear Discriminant Analysis or randomForest

### Description

visualization of effect size by the Linear Discriminant Analysis or randomForest

### Usage

    ggeffectsize(obj, ...)

    ## S3 method for class 'data.frame'
    ggeffectsize(
      obj,
      factorName,
      effectsizename,
      factorLevels = NULL,
      linecolor = "grey50",
      linewidth = 0.4,
      lineheight = 0.2,
      pointsize = 1.5,
      setFacet = TRUE,
      ...
    )

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

### Arguments

`obj` | object, diffAnalysisClass see `diff_analysis`, or data.frame, contained effect size and the group information.
`...` | additional arguments.
`factorName` | character, the column name contained group information in data.frame.
`effectsizename` | character, the column name contained effect size information.
`factorLevels` | list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.
`linecolor` | character, the color of horizontal error bars, default is grey50.
`linewidth` | numeric, the width of horizontal error bars, default is 0.4.
`lineheight` | numeric, the height of horizontal error bars, default is 0.2.
`pointsize` | numeric, the size of points, default is 1.5.
`setFacet` | logical, whether use facet to plot, default is TRUE.
`removeUnknown` | logical, whether do not show unknown taxonomy, default is TRUE.

### Value

the figures of effect size show the LDA or MDA (MeanDecreaseAccuracy).

### 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)
    #effectplot <- ggeffectsize(diffres) +
    #              scale_color_manual(values=c('#00AED7',
    #                                          '#FD9347',
    #                                          '#C1E168'))+
    #              theme_bw()+
    #              theme(strip.background=element_rect(fill=NA),
    #                    panel.spacing = unit(0.2, "mm"),
    #                    panel.grid=element_blank(),
    #                    strip.text.y=element_blank())

[Package MicrobiotaProcess version 1.2.2 Index]