pairsplot: Draw multiple bi-plots.

Description Usage Arguments Details Value Author(s) Examples

View source: R/pairsplot.R

Description

Draw multiple bi-plots.

Usage

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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,
  labhjust = 1.5,
  labvjust = 0,
  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.

labhjust

Horizontal adjustment of label.

labvjust

Vertical adjustment of label.

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 <kevin@clinicalbioinformatics.co.uk>

Examples

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  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)

PCAtools documentation built on Nov. 8, 2020, 8:17 p.m.