prot.plot_screeplot: SCREE plot

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

SCREE plot

Description

prot.plot_screeplot() creates a SCREE plot of the explained variation in the principal components of a 'princomp' object

Usage

prot.plot_screeplot(
  pcaobj,
  components,
  xlim = NULL,
  ylim = c(0, 100),
  xlab = "Principal component",
  xlabAngle = 90,
  xlabhjust = 0.5,
  xlabvjust = 0.5,
  ylab = "Explained variation (%)",
  ylabAngle = 0,
  ylabhjust = 0.5,
  ylabvjust = 0.5,
  axisLabSize = 16,
  title = "SCREE plot",
  subtitle = "",
  caption = "",
  titleLabSize = 16,
  subtitleLabSize = 12,
  captionLabSize = 12,
  colBar = "dodgerblue",
  drawCumulativeSumLine = TRUE,
  colCumulativeSumLine = "red2",
  sizeCumulativeSumLine = 1.5,
  drawCumulativeSumPoints = TRUE,
  colCumulativeSumPoints = "red2",
  sizeCumulativeSumPoints = 2,
  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",
  plot = TRUE,
  export = TRUE
)

Arguments

pcaobj	An object of class 'princomp'
components	A numeric vector of principal component numbers to include in the plot
xlim	A numeric vector of length 2 specifying the x-axis limits
ylim	A numeric vector of length 2 specifying the y-axis limits. Default is c(0, 100)
xlab	A character string for x-axis label
xlabAngle	Numeric value for x-axis label angle
xlabhjust	Numeric value for x-axis label horizontal justification
xlabvjust	Numeric value for x-axis label vertical justification
ylab	A character string for y-axis label
ylabAngle	Numeric value for y-axis label angle
ylabhjust	Numeric value for y-axis label horizontal justification
ylabvjust	Numeric value for y-axis label vertical justification
axisLabSize	Numeric value for axis label size
title	A character string for the plot title
subtitle	A character string for the plot subtitle
caption	A character string for the plot caption
titleLabSize	Numeric value for title label size
subtitleLabSize	Numeric value for subtitle label size
captionLabSize	Numeric value for caption label size
colBar	A character string for the color of the bar chart
drawCumulativeSumLine	Logical value to indicate if the cumulative sum line should be plotted
colCumulativeSumLine	A character string for the color of the cumulative sum line
sizeCumulativeSumLine	Numeric value for the size of the cumulative sum line
drawCumulativeSumPoints	Logical value to indicate if the cumulative sum points should be plotted
colCumulativeSumPoints	A character string for the color of the cumulative sum points
sizeCumulativeSumPoints	Numeric value for the size of the cumulative sum points
hline	A numeric value for horizontal line
hlineType	A character string for the type of horizontal line
hlineCol	A character string for the color of the horizontal line
hlineWidth	Numeric value for the width of the horizontal line
vline	A numeric value for vertical line
vlineType	A character string for the type of vertical line
vlineCol	A character string for the color of the vertical line
vlineWidth	Numeric value for the width of the vertical line
gridlines.major	Logical value to indicate if major gridlines should be plotted
gridlines.minor	Logical value to indicate if minor gridlines should be plotted
borderWidth	Numeric value for the width of the border
borderColour	A character string for the color of the border
plot	Logical value to indicate if the plot should be plotted
export	Logical value to indicate if the plot should be exported as PNG and PDF

Value

A SCREE plot

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.