plot.combi: Make multiplots of the data integration object

View source: R/plot.combi.R

plot.combiR Documentation

Make multiplots of the data integration object

Description

Make multiplots of the data integration object

Usage

## S3 method for class 'combi'
plot(
  x,
  ...,
  Dim = c(1, 2),
  samDf = NULL,
  samShape = NULL,
  samCol = NULL,
  featurePlot = "threshold",
  featNum = 15L,
  samColValues = NULL,
  manExpFactorTaxa = 0.975,
  featSize = switch(featurePlot, threshold = 2.5, points = samSize * 0.7, density = 0.35),
  crossSize = 4,
  manExpFactorVar = 0.975,
  varNum = nrow(x$alphas),
  varSize = 2.5,
  samSize = 1.75,
  featCols = c("darkblue", "darkgreen", "grey10", "turquoise4", "blue", "green", "grey",
    "cornflowerblue", "lightgreen", "grey75"),
  strokeSize = 0.05,
  warnMonotonicity = FALSE,
  returnCoords = FALSE,
  squarePlot = TRUE,
  featAlpha = 0.5,
  featShape = 8,
  xInd = 0,
  yInd = 0,
  checkOverlap = FALSE,
  shapeValues = (21:(21 + length(unique(samDf[[samShape]]))))
)

Arguments

x

the fit

...

additional arguments, currently ignored

Dim

the dimensions to be plotted

samDf

a dataframe of sample variables

samShape

A variable name from samDf used to shape the samples

samCol

A variable name from samDf used to colour the samples

featurePlot

A character string, either "threshold", "points" or "density". See details

featNum, varNum

The number of features and variables to plot

samColValues

Colours for the samples

manExpFactorTaxa, manExpFactorVar

Expansion factors for taxa and variables, normally calculated natively

featSize, crossSize, varSize, samSize, strokeSize

Size parameters for the features (text, dots or density contour lines), central cross, variable labels, sample dots, sample strokes and feature contour lines

featCols

Colours for the features

warnMonotonicity

A boolean, should a warning be thrown when the feature proportions of compositional views do not all vary monotonically with all latent variables?

returnCoords

A boolean, should coordinates be returned, e.g. for use in thrird party software

squarePlot

A boolean, should the axes be square? Strongly recommended

featAlpha

Controls the transparacny of the features

featShape

Shape of feature dots when featurePlot = "points"

xInd, yInd

x and y indentations

checkOverlap

A boolean, should overlapping labels be omitted?

shapeValues

the shapes, as numeric values

Details

It is usually impossible to plot all features with their labels. Therefore, he default option of the 'featurePlot' parameter is "threshold", whereby only the 'featNum" features furthest away from the origin are shown. Alternatively, the "points" or "density" options are available to plot all features as a point or density cloud, but without labels.

Value

A ggplot object containing the plot

Examples

data(Zhang)
## Not run: 
#Unconstrained
microMetaboInt = combi(
list("microbiome" = zhangMicrobio, "metabolomics" = zhangMetabo),
distributions = c("quasi", "gaussian"), compositional = c(TRUE, FALSE),
logTransformGaussian = FALSE, verbose = TRUE)
#Constrained
microMetaboIntConstr = combi(
    list("microbiome" = zhangMicrobio, "metabolomics" = zhangMetabo),
    distributions = c("quasi", "gaussian"), compositional = c(TRUE, FALSE),
    logTransformGaussian = FALSE, covariates = zhangMetavars, verbose = TRUE)
## End(Not run)
    #Load the fits
load(system.file("extdata", "zhangFits.RData", package = "combi"))
plot(microMetaboInt)
plot(microMetaboInt, samDf = zhangMetavars, samCol = "ABX")
#Plot all features as points or density
plot(microMetaboInt, samDf = zhangMetavars, samCol = "ABX",
featurePlot = "points")
plot(microMetaboInt, samDf = zhangMetavars, samCol = "ABX",
featurePlot = "density")
#Constrained
plot(microMetaboIntConstr, samDf = zhangMetavars, samCol = "ABX")

CenterForStatistics-UGent/combi documentation built on Aug. 22, 2023, 11:02 p.m.