volcanoPlotPlus: generates a volcano plot of a data.frame with quantification...

In BenBruyneel/BBPersonalR: BBPersonalR

generates a volcano plot of a data.frame with quantification data & statisitcal significance data. Additionally the distributions of the quantification and the statistical data are shown via density plots (and optionally a qqplot)

Description

generates a volcano plot of a data.frame with quantification data & statisitcal significance data. Additionally the distributions of the quantification and the statistical data are shown via density plots (and optionally a qqplot)

Usage

volcanoPlotPlus(
  data,
  quantColumn = 1,
  statColumn = 2,
  xLabel = ifelse(is.character(quantColumn), paste(c("Log2 ", quantColumn), collapse =
    ""), paste(c("Log2 ", colnames(data)[quantColumn]), collapse = "")),
  yLabel = ifelse(is.character(statColumn), paste(c("-Log10 ", statColumn), collapse =
    ""), paste(c("-Log10 ", colnames(data)[statColumn]), collapse = "")),
  xCutoffs = c(0.5, 2),
  yCutoff = 0.05,
  title = "",
  gridLines = TRUE,
  volcanoLineMarkers = volcanoLineMarkerDedaults(),
  volcanoLineMarkerAttributes = volcanoMarkerAttributesDefaults(),
  returnData = FALSE,
  significanceColumnName = "",
  removeNonSignificantData = TRUE,
  identifierColumn = NA,
  showQQPlot = TRUE,
  widths = c(125, 875),
  heights = c(875, 125),
  ...
)

Arguments

data	data.frame with at least two columns
quantColumn	specifies which column in the data argument contains the quantification data (can be number or character vector)
statColumn	specifies which column in the data argument contains the statistical significance data (can be number or character vector). Usually these values are p-values from eg a t-test
xLabel	defines x-axis label
yLabel	defines y-axis label
xCutoffs	minimum and maximum value of the quantColumn data (before transformation). Anything outside these values and lower than yCutoff will be marked as significant
yCutoff	minimum value of the statColumn data. any value lower is marked as significant (usually p-value < 0.05)
title	specifies the title
gridLines	if TRUE then gridlines are shown
volcanoLineMarkers	defines where to place marker lines in the plot
volcanoLineMarkerAttributes	defines the attributes of the marker lines
returnData	if TRUE then a list with 2 elements is returned. The first element is the data.frame used to generate the graph and the second element is the graph itself
significanceColumnName	name to give to the column specifying if a row is significant (TRUE) or (FALSE). If not specified, then the name "significant" will be used
removeNonSignificantData	if TRUE, no non-significant data will be returned (usually a smaller data.frame to return). If FALSE then all data will be returned
identifierColumn	specifies which columns from data (names -> character vector) should be included in the data.frame returned
showQQPlot	if TRUE then a qq plot of the x-axis (after transformation) is shown in the left bottom corner
widths	horizontal: two number (integer) vector specifying the amount of the plot to be used for the volcanoplot and the amount for the density plot
heights	vertical: two number (integer) vector specifying the amount of the plot to be used for the volcanoplot and the amount for the density plot
...	can be used to pass on other arguments to graphAdjust()

Value

a ggplot object or a list

Note

what is returned is grobtable (class gtable): this can be drawn via the grid.draw() function. The plot drawn before this will have to be cleared "manually" via clearPlot()

BenBruyneel/BBPersonalR documentation built on Aug. 23, 2024, 8:28 p.m.