pairsplot: Draw multiple bi-plots.

In kevinblighe/PCAtools: PCAtools: Everything Principal Components Analysis

Draw multiple bi-plots.

Description

Draw multiple bi-plots.

Usage

pairsplot(
  pcaobj,
  components = getComponents(pcaobj, seq_len(5)),
  triangle = TRUE,
  trianglelabSize = 18,
  plotaxes = TRUE,
  margingaps = unit(c(0.1, 0.1, 0.1, 0.1), "cm"),
  ncol = NULL,
  nrow = NULL,
  x = NULL,
  y = NULL,
  colby = NULL,
  colkey = NULL,
  singlecol = NULL,
  shape = NULL,
  shapekey = NULL,
  pointSize = 1,
  legendPosition = "none",
  legendLabSize = 6,
  legendIconSize = 1.5,
  xlim = NULL,
  ylim = NULL,
  lab = NULL,
  labSize = 1.5,
  selectLab = NULL,
  drawConnectors = FALSE,
  widthConnectors = 0.5,
  colConnectors = "grey50",
  xlab = NULL,
  xlabAngle = 0,
  xlabhjust = 0.5,
  xlabvjust = 0.5,
  ylab = NULL,
  ylabAngle = 0,
  ylabhjust = 0.5,
  ylabvjust = 0.5,
  axisLabSize = 10,
  title = NULL,
  titleLabSize = 32,
  hline = NULL,
  hlineType = "longdash",
  hlineCol = "black",
  hlineWidth = 0.4,
  vline = NULL,
  vlineType = "longdash",
  vlineCol = "black",
  vlineWidth = 0.4,
  gridlines.major = TRUE,
  gridlines.minor = TRUE,
  borderWidth = 0.8,
  borderColour = "black",
  returnPlot = TRUE
)

Arguments

pcaobj	Object of class 'pca' created by pca().
components	The principal components to be included in the plot. These will be compared in a pairwise fashion via multiple calls to biplot().
triangle	Logical, indicating whether or not to draw the plots in the upper panel in a triangular arrangement? Principal component names will be labeled along the diagonal.
trianglelabSize	Size of p rincipal component label (when triangle = TRUE).
plotaxes	Logical, indicating whether or not to draw the axis tick, labels, and titles.
margingaps	The margins between plots in the plot space. Takes the form of a 'unit()' variable.
ncol	If triangle = FALSE, the number of columns in the final merged plot.
nrow	If triangle = FALSE, the number of rows in the final merged plot.
x	A principal component to plot on x-axis. All principal component names are stored in pcaobj$label.
y	A principal component to plot on y-axis. All principal component names are stored in pcaobj$label.
colby	If NULL, all points will be coloured differently. If not NULL, value is assumed to be a column name in pcaobj$metadata relating to some grouping/categorical variable.
colkey	Vector of name-value pairs relating to value passed to 'col', e.g., c(A='forestgreen', B='gold').
singlecol	If specified, all points will be shaded by this colour. Overrides 'col'.
shape	If NULL, all points will be have the same shape. If not NULL, value is assumed to be a column name in pcaobj$metadata relating to some grouping/categorical variable.
shapekey	Vector of name-value pairs relating to value passed to 'shape', e.g., c(A=10, B=21).
pointSize	Size of plotted points.
legendPosition	Position of legend ('top', 'bottom', 'left', 'right', 'none').
legendLabSize	Size of plot legend text.
legendIconSize	Size of plot legend icons / symbols.
xlim	Limits of the x-axis.
ylim	Limits of the y-axis.
lab	A vector containing labels to add to the plot.
labSize	Size of labels.
selectLab	A vector containing a subset of lab to plot.
drawConnectors	Logical, indicating whether or not to connect plot labels to their corresponding points by line connectors.
widthConnectors	Line width of connectors.
colConnectors	Line colour of connectors.
xlab	Label for x-axis.
xlabAngle	Rotation angle of x-axis labels.
xlabhjust	Horizontal adjustment of x-axis labels.
xlabvjust	Vertical adjustment of x-axis labels.
ylab	Label for y-axis.
ylabAngle	Rotation angle of y-axis labels.
ylabhjust	Horizontal adjustment of y-axis labels.
ylabvjust	Vertical adjustment of y-axis labels.
axisLabSize	Size of x- and y-axis labels.
title	Plot title.
titleLabSize	Size of plot title.
hline	Draw one or more horizontal lines passing through this/these values on y-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90).
hlineType	Line type for hline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash').
hlineCol	Colour of hline.
hlineWidth	Width of hline.
vline	Draw one or more vertical lines passing through this/these values on x-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90).
vlineType	Line type for vline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash').
vlineCol	Colour of vline.
vlineWidth	Width of vline.
gridlines.major	Logical, indicating whether or not to draw major gridlines.
gridlines.minor	Logical, indicating whether or not to draw minor gridlines.
borderWidth	Width of the border on the x and y axes.
borderColour	Colour of the border on the x and y axes.
returnPlot	Logical, indicating whether or not to return the plot object.

Details

Draw multiple bi-plots.

Value

A cowplot object.

Author(s)

Kevin Blighe <[e-mail]>

Examples

  options(scipen=10)
  options(digits=6)

  col <- 20
  row <- 20000
  mat1 <- matrix(
    rexp(col*row, rate = 0.1),
    ncol = col)
  rownames(mat1) <- paste0('gene', 1:nrow(mat1))
  colnames(mat1) <- paste0('sample', 1:ncol(mat1))

  mat2 <- matrix(
    rexp(col*row, rate = 0.1),
    ncol = col)
  rownames(mat2) <- paste0('gene', 1:nrow(mat2))
  colnames(mat2) <- paste0('sample', (ncol(mat1)+1):(ncol(mat1)+ncol(mat2)))

  mat <- cbind(mat1, mat2)

  metadata <- data.frame(row.names = colnames(mat))
  metadata$Group <- rep(NA, ncol(mat))
  metadata$Group[seq(1,40,2)] <- 'A'
  metadata$Group[seq(2,40,2)] <- 'B'
  metadata$CRP <- sample.int(100, size=ncol(mat), replace=TRUE)
  metadata$ESR <- sample.int(100, size=ncol(mat), replace=TRUE)

  p <- pca(mat, metadata = metadata, removeVar = 0.1)

  pairsplot(p, triangle = TRUE)

kevinblighe/PCAtools documentation built on Oct. 22, 2023, 12:01 p.m.