ggordpoint: ordination plotter based on ggplot2.

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

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,
  showsample = FALSE,
  ellipse_pro = 0.9,
  ellipse_alpha = 0.2,
  ellipse_linewd = 0.5,
  ellipse_lty = 3,
  biplot = FALSE,
  topn = 5,
  settheme = TRUE,
  speciesannot = FALSE,
  fontsize = 2.5,
  labelfactor = NULL,
  stroke = 0.1,
  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 when your want to set it by yourself, only alpha can be setted, and the first element of factorNames has been setted to map 'fill', and the second element of factorNames has been setted to map 'starshape', you can add 'scale_starshape_manual' of 'ggstar' to set the shapes.
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.
showsample	logical, whether show the labels of sample, 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.
ellipse_linewd	numeric, the width of ellipse line, default is 0.5.
ellipse_lty	integer, the type of ellipse line, default is 3
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.
labelfactor	character, the factor want to be show in label, default is NULL.
stroke	numeric, the line size of points, default is 0.1.
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

## Not run: 
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)

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.