PCAtools (version 1.3.6)

biplot: biplot

Description

Draw a bi-plot, comparing 2 selected principal components / eigenvectors.

Usage

biplot(pcaobj,
  x = 'PC1',
  y = 'PC2',
  colby = NULL,
  colkey = NULL,
  singlecol = NULL,
  shape = NULL,
  shapekey = NULL,
  pointSize = 3.0,
  legendPosition = 'none',
  legendLabSize = 12,
  legendIconSize = 5.0,
  xlim = NULL,
  ylim = NULL,
  lab = rownames(pcaobj$metadata),
  labSize = 3.0,
  labhjust = 1.5,
  labvjust = 0,
  selectLab = NULL,
  drawConnectors = TRUE,
  widthConnectors = 0.5,
  colConnectors = 'grey50',
  xlab = paste0(x, ', ',
    round(pcaobj$variance[x], digits=2),
    '% variation'),
  xlabAngle = 0,
  xlabhjust = 0.5,
  xlabvjust = 0.5,
  ylab = paste0(y, ', ',
    round(pcaobj$variance[y], digits=2),
    '% variation'),
  ylabAngle = 0,
  ylabhjust = 0.5,
  ylabvjust = 0.5,
  axisLabSize = 16,
  title = '',
  subtitle = '',
  caption = '',
  titleLabSize = 16,
  subtitleLabSize = 12,
  captionLabSize = 12,
  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(). REQUIRED.

x

A principal component to plot on x-axis. All principal component names are stored in pcaobj$label. DEFAULT = 'PC1'. REQUIRED.

y

A principal component to plot on y-axis. All principal component names are stored in pcaobj$label. DEFAULT = 'PC2'. REQUIRED.

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. DEFAULT = NULL. OPTIONAL.

colkey

Vector of name-value pairs relating to value passed to 'col', e.g., c(A='forestgreen', B='gold'). DEFAULT = NULL. OPTIONAL.

singlecol

If specified, all points will be shaded by this colour. Overrides 'col'. DEFAULT = NULL. OPTIONAL.

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. DEFAULT = NULL. OPTIONAL.

shapekey

Vector of name-value pairs relating to value passed to 'shape', e.g., c(A=10, B=21). DEFAULT = NULL. OPTIONAL.

pointSize

Size of plotted points. DEFAULT = 3.0. OPTIONAL.

legendPosition

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

lab

A vector containing labels to add to the plot. DEFAULT = rownames(pcaobj$metadata). OPTIONAL.

labSize

Size of labels. DEFAULT = 3.0. OPTIONAL.

labhjust

Horizontal adjustment of label. DEFAULT = 1.5. OPTIONAL.

labvjust

Vertical adjustment of label. DEFAULT = 0. OPTIONAL.

selectLab

A vector containing a subset of lab to plot. DEFAULT = NULL. OPTIONAL.

drawConnectors

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

widthConnectors

Line width of connectors. DEFAULT = 0.5. OPTIONAL.

colConnectors

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

xlab

Label for x-axis. DEFAULT = paste0(x, ', ', round(pcaobj$variance[x], digits=2), '% variation'). 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 = paste0(y, ', ', round(pcaobj$variance[y], digits=2), '% variation'). 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 = NULL. 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)

  biplot(p)

  biplot(p, colby = 'Group', shape = 'Group')

  biplot(p, colby = 'Group', colkey = c(A = 'forestgreen', B = 'gold'),
    legendPosition = 'right')

  biplot(p, colby = 'Group', colkey = c(A='forestgreen', B='gold'),
    shape = 'Group', shapekey = c(A=10, B=21), legendPosition = 'bottom')

# }