ggordpoint {MicrobiotaProcess} | R Documentation

## ordination plotter based on ggplot2.

### Description

ordination plotter based on ggplot2.

### Usage

    ggordpoint(obj, ...)

    ## Default S3 method:
    ggordpoint(
      obj,
      pc = c(1, 2),
      mapping = NULL,
      sampleda = NULL,
      factorNames = NULL,
      factorLevels = NULL,
      poinsize = 2,
      linesize = 0.3,
      arrowsize = 1.5,
      arrowlinecolour = "grey",
      ellipse = FALSE,
      ellipse_pro = 0.9,
      ellipse_alpha = 0.2,
      biplot = FALSE,
      topn = 5,
      settheme = TRUE,
      speciesannot = FALSE,
      fontsize = 2.5,
      fontface = "bold.italic",
      fontfamily = "sans",
      textlinesize = 0.02,
      ...
    )

    ## S3 method for class 'pcasample'
    ggordpoint(obj, ...)

### Arguments

`obj` | prcomp class or pcasample class,
`...` | additional parameters, see `geom_text_repel`.
`pc` | integer vector, the component index.
`mapping` | set of aesthetic mapping of ggplot2, default is NULL.
`sampleda` | data.frame, nrow sample * ncol factors, default is NULL.
`factorNames` | vector, the names of factors contained sampleda.
`factorLevels` | list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.
`poinsize` | numeric, the size of point, default is 2.
`linesize` | numeric, the line size of segment, default is 0.3.
`arrowsize` | numeric, the size of arrow, default is 1.5.
`arrowlinecolour` | character, the color of segment, default is grey.
`ellipse` | logical, whether add confidence ellipse to ordinary plot, default is FALSE.
`ellipse_pro` | numeric, confidence value for the ellipse, default is 0.9.
`ellipse_alpha` | numeric, the alpha of ellipse, default is 0.2.
`biplot` | logical, whether plot the species, default is FALSE.
`topn` | integer or vector, the number species have top important contribution, default is 5.
`settheme` | logical, whether set the theme for the plot, default is TRUE.
`speciesannot` | logical, whether plot the species, default is FALSE.
`fontsize` | numeric, the size of text, default is 2.5.
`fontface` | character, the font face, default is "blod.italic".
`fontfamily` | character, the font family, default is "sans".
`textlinesize` | numeric, the segment size in `geom_text_repel`.

### Value

point figures of PCA or PCoA.

### Author(s)

Shuangbin Xu

### Examples

    #don't run in examples
    #library(phyloseq)
    #data(GlobalPatterns)
    #subGlobal <- subset_samples(GlobalPatterns,
    #         SampleType %in% c("Feces", "Mock", "Ocean", "Skin"))
    #pcares <- get_pca(subGlobal, method="hellinger")
    #pcaplot <- ggordpoint(pcares, biplot=TRUE,
    #                    speciesannot=TRUE,
    #                     factorNames=c("SampleType"), ellipse=TRUE)

[Package MicrobiotaProcess version 1.0.5 Index]