PCAtools (version 1.3.6)

plotloadings: plotloadings

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 = 3.0,
  xlim = NULL,
  ylim = NULL,
  labSize = 2.0,
  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(). REQUIRED.

components

The principal components to be included in the plot. DEFAULT = getComponents(pcaobj, seq_len(5)). OPTIONAL.

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. DEFAULT = 0.05. OPTIONAL.

absolute

Logical, indicating whether or not to plot absolute loadings. DEFAULT = FALSE. OPTIONAL.

col

Colours used for generation of fill gradient according to loadings values. Can be 2 or 3 colours. DEFAULT = c('gold', 'white', 'royalblue'). OPTIONAL.

colMidpoint

Mid-point (loading) for the colour range. DEFAULT = 0. OPTIONAL.

shape

Shape of the plotted points. DEFAULT = 21. OPTIONAL.

shapeSizeRange

Size range for the plotted points (min, max). DEFAULT = c(10, 10). OPTIONAL.

legendPosition

Position of legend ('top', 'bottom', 'left', 'right', 'none'). DEFAULT = 'top'. OPTIONAL.

legendLabSize

Size of plot legend text. DEFAULT = 10. OPTIONAL.

legendIconSize

Size of plot legend icons / symbols. DEFAULT = 3.0. OPTIONAL.

xlim

Limits of the x-axis. DEFAULT = NULL. OPTIONAL.

ylim

Limits of the y-axis. DEFAULT = NULL. OPTIONAL.

labSize

Size of labels. DEFAULT = 2.0. OPTIONAL.

labhjust

Horizontal adjustment of label. DEFAULT = 1.5. OPTIONAL.

labvjust

Vertical adjustment of label. DEFAULT = 0. OPTIONAL.

drawConnectors

Logical, indicating whether or not to connect plot labels to their corresponding points by line connectors. DEFAULT = TRUE. OPTIONAL.

positionConnectors

Position of the connectors and their labels with respect to the plotted points ('left', 'right'). DEFAULT = 'right'. OPTIONAL.

widthConnectors

Line width of connectors. DEFAULT = 0.5. OPTIONAL.

typeConnectors

Have the arrow head open or filled ('closed')? ('open', 'closed'). DEFAULT = 'closed'. OPTIONAL.

endsConnectors

Which end of connectors to draw arrow head? ('last', 'first', 'both'). DEFAULT = 'first'. OPTIONAL.

lengthConnectors

Length of the connectors. DEFAULT = unit(0.01, 'npc'). OPTIONAL

colConnectors

Line colour of connectors. DEFAULT = 'grey50'. OPTIONAL.

xlab

Label for x-axis. DEFAULT = 'Principal component'. OPTIONAL.

xlabAngle

Rotation angle of x-axis labels. DEFAULT = 0. OPTIONAL.

xlabhjust

Horizontal adjustment of x-axis labels. DEFAULT = 0.5. OPTIONAL.

xlabvjust

Vertical adjustment of x-axis labels. DEFAULT = 0.5. OPTIONAL.

ylab

Label for y-axis. DEFAULT = 'Component loading'. OPTIONAL.

ylabAngle

Rotation angle of y-axis labels. DEFAULT = 0. OPTIONAL.

ylabhjust

Horizontal adjustment of y-axis labels. DEFAULT = 0.5. OPTIONAL.

ylabvjust

Vertical adjustment of y-axis labels. DEFAULT = 0.5. OPTIONAL.

axisLabSize

Size of x- and y-axis labels. DEFAULT = 16. OPTIONAL.

title

Plot title. DEFAULT = ''. OPTIONAL.

subtitle

Plot subtitle. DEFAULT = ''. OPTIONAL.

caption

Plot caption. DEFAULT = ''. OPTIONAL.

titleLabSize

Size of plot title. DEFAULT = 16. OPTIONAL.

subtitleLabSize

Size of plot subtitle. DEFAULT = 12. OPTIONAL.

captionLabSize

Size of plot caption. DEFAULT = 12. OPTIONAL.

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). DEFAULT = c(0). OPTIONAL.

hlineType

Line type for hline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash'). DEFAULT = 'longdash'. OPTIONAL.

hlineCol

Colour of hline. DEFAULT = 'black'. OPTIONAL.

hlineWidth

Width of hline. DEFAULT = 0.4. OPTIONAL.

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). DEFAULT = NULL. OPTIONAL.

vlineType

Line type for vline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash'). DEFAULT = 'longdash'. OPTIONAL.

vlineCol

Colour of vline. DEFAULT = 'black'. OPTIONAL.

vlineWidth

Width of vline. DEFAULT = 0.4. OPTIONAL.

gridlines.major

Logical, indicating whether or not to draw major gridlines. DEFAULT = TRUE. OPTIONAL.

gridlines.minor

Logical, indicating whether or not to draw minor gridlines. DEFAULT = TRUE. OPTIONAL.

borderWidth

Width of the border on the x and y axes. DEFAULT = 0.8. OPTIONAL.

borderColour

Colour of the border on the x and y axes. DEFAULT = 'black'. OPTIONAL.

returnPlot

Logical, indicating whether or not to return the plot object. DEFAULT = TRUE. OPTIONAL.

Value

A ggplot2 object.

Examples

# NOT RUN {
  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)
# }