Plot the loadings of a principal components analysis

Usage

prot.plot_loadings(
  pcaobj,
  components = PCAtools::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",
  plot = TRUE,
  export = TRUE
)

Arguments

pcaobj: An object that contains the results of a PCA analysis.
components: The components to plot. Defaults to the first 5 components.
rangeRetain: a numeric value between 0 and 1 indicating the proportion of loading values to retain. Default is 0.05.
absolute: a logical value indicating whether to plot absolute loading values (TRUE) or signed loading values (FALSE). Default is FALSE.
col: a vector of colors for the points on the plot. Default is c("gold", "white", "royalblue").
colMidpoint: a numeric value indicating the midpoint for the color gradient. Default is 0.
shape: an integer indicating the shape of the points on the plot. Default is 21.
shapeSizeRange: a numeric vector of length 2 indicating the range of point sizes. Default is c(10, 10).
legendPosition: a character string indicating the position of the legend. Default is "top".
legendLabSize: an integer indicating the size of the legend labels. Default is 10.
legendIconSize: a numeric value indicating the size of the legend icons. Default is 3.
xlim: a numeric vector of length 2 indicating the range of the x-axis. Default is NULL.
ylim: a numeric vector of length 2 indicating the range of the y-axis. Default is NULL.
labSize: an integer indicating the size of the point labels. Default is 2.
labhjust: a numeric value indicating the horizontal justification of the point labels. Default is 1.5.
labvjust: a numeric value indicating the vertical justification of the point labels. Default is 0.
drawConnectors: a logical value indicating whether to draw connectors between points. Default is TRUE.
positionConnectors: a character string indicating the position of the connectors. Default is "right".
widthConnectors: a numeric value indicating the width of the connectors. Default is 0.5.
typeConnectors: a character string indicating the type of the connectors. Default is "closed".
endsConnectors: a character string indicating the ends of the connectors. Default is "first".
lengthConnectors: a numeric value indicating the length of the connectors. Default is unit(0.01, "npc").
colConnectors: a character string indicating the color of the connectors. Default is "grey50".
xlab: a character string indicating the label for the x-axis. Default is "Principal component".
xlabAngle: a numeric value indicating the angle of the x-axis label. Default is 0.
xlabhjust: a numeric value indicating the horizontal justification of the x-axis label. Default is 0.5.
xlabvjust: a numeric value indicating the vertical justification of the x-axis label. Default is 0.5.
ylab: a character string indicating the label for the y-axis. Default is "Component loading".
ylabAngle: a numeric value indicating the angle of the y-axis label. Default is 0.
ylabhjust: a numeric value indicating the horizontal justification of the y-axis label. Default is 0.5.
ylabvjust: a numeric value indicating the vertical justification of the y-axis label. Default is 0.5.
axisLabSize: an integer indicating the size of the axis labels. Default is 16.
title: a character string indicating the title of the plot. Default is an empty string.
subtitle: a character string indicating the subtitle of the plot. Default is an empty string.
caption: a character string indicating the caption of the plot. Default is an empty string.
titleLabSize: an integer indicating the size of the title label. Default is 16.
subtitleLabSize: an integer indicating the size of the subtitle label. Default is 12.
captionLabSize: an integer indicating the size of the caption label. Default is 12.
hline: a numeric vector indicating the horizontal lines to be plotted. Default is c(0).
hlineType: a character string indicating the type of the horizontal lines. Default is "longdash".
hlineCol: a character string indicating the color of the horizontal lines. Default is "black".
hlineWidth: a numeric value indicating the width of the horizontal lines. Default is 0.4.
vline: a numeric vector indicating the vertical lines to be plotted. Default is NULL.
vlineType: a character string indicating the type of the vertical lines. Default is "longdash".
vlineCol: a character string indicating the color of the vertical lines. Default is "black".
vlineWidth: a numeric value indicating the width of the vertical lines. Default is 0.4.
gridlines.major: a logical value indicating whether to show major gridlines. Default is TRUE.
gridlines.minor: a logical value indicating whether to show minor gridlines. Default is TRUE.
borderWidth: a numeric value indicating the width of the border. Default is 0.8.
borderColour: a character string indicating the color of the border. Default is "black".
plot: a logical value indicating whether to plot the graph. Default is TRUE.
export: a logical value indicating whether to export the plot. Default is TRUE.

Value

a scatter plot of the loading values for each gene/protein for the specified principal components in a PCA object.