plotloadings: Plot the component loadings for selected principal components...

In kevinblighe/PCAtools: PCAtools: Everything Principal Components Analysis

Plot the component loadings for selected principal components / eigenvectors and label variables driving variation along these.

Description

Plot the component loadings for selected principal components / eigenvectors and label variables driving variation along these.

Usage

plotloadings(
  pcaobj,
  components = getComponents(pcaobj, seq_len(5)),
  rangeRetain = 0.05,
  absolute = FALSE,
  col = c("gold", "white", "royalblue"),
  colMidpoint = 0,
  shape = 21,
  shapeSizeRange = c(10, 10),
  legendPosition = "top",
  legendLabSize = 10,
  legendIconSize = 3,
  xlim = NULL,
  ylim = NULL,
  labSize = 2,
  labhjust = 1.5,
  labvjust = 0,
  drawConnectors = TRUE,
  positionConnectors = "right",
  widthConnectors = 0.5,
  typeConnectors = "closed",
  endsConnectors = "first",
  lengthConnectors = unit(0.01, "npc"),
  colConnectors = "grey50",
  xlab = "Principal component",
  xlabAngle = 0,
  xlabhjust = 0.5,
  xlabvjust = 0.5,
  ylab = "Component loading",
  ylabAngle = 0,
  ylabhjust = 0.5,
  ylabvjust = 0.5,
  axisLabSize = 16,
  title = "",
  subtitle = "",
  caption = "",
  titleLabSize = 16,
  subtitleLabSize = 12,
  captionLabSize = 12,
  hline = c(0),
  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.
rangeRetain	Cut-off value for retaining variables. The function will look across each specified principal component and retain the variables that fall within this top/bottom fraction of the loadings range.
absolute	Logical, indicating whether or not to plot absolute loadings.
col	Colours used for generation of fill gradient according to loadings values. Can be 2 or 3 colours.
colMidpoint	Mid-point (loading) for the colour range.
shape	Shape of the plotted points.
shapeSizeRange	Size range for the plotted points (min, max).
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.
labSize	Size of labels.
labhjust	Horizontal adjustment of label.
labvjust	Vertical adjustment of label.
drawConnectors	Logical, indicating whether or not to connect plot labels to their corresponding points by line connectors.
positionConnectors	Position of the connectors and their labels with respect to the plotted points ('left', 'right').
widthConnectors	Line width of connectors.
typeConnectors	Have the arrow head open or filled ('closed')? ('open', 'closed').
endsConnectors	Which end of connectors to draw arrow head? ('last', 'first', 'both').
lengthConnectors	Length of the 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.
subtitle	Plot subtitle.
caption	Plot caption.
titleLabSize	Size of plot title.
subtitleLabSize	Size of plot subtitle.
captionLabSize	Size of plot caption.
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

Plot the component loadings for selected principal components / eigenvectors and label variables driving variation along these.

Value

A ggplot2 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)

  plotloadings(p, drawConnectors = TRUE)

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