plotloadings {PCAtools} | R Documentation

## 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.

### Author(s)

Kevin Blighe <kevin@clinicalbioinformatics.co.uk>, Myles Lewis <myles.lewis@qmul.ac.uk>

### 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)

[Package PCAtools version 1.0.0 Index]