plotPlate: Plot the layout or measurements on each screening plate

In lujunyan1118/DrugScreenExplorer_dev: A pipeline for processing drug sensitivity screen data

Description

This function generates a heatmap or a series of heatmaps showing the plate layout, raw intensity or normalized intensity for each plate in the screen dataset.

Usage

plotPlate(
  screenData,
  plotPlate = "all",
  plotType = "layout",
  ifCorrected = FALSE,
  limits = NULL,
  pdfName = NULL,
  ncol = 2,
  nrow = 3,
  width = 16,
  height = 16
)

Arguments

screenData	a data frame containing screen data generated by readScreen() function
plotPlate	a character string or a vector of character strings specifying the file name of the plates. If all plates should be included, 'all' can be used. Default value is 'all'
plotType	a character string specifying the type of the plot, one of 'layout', 'zscore' and 'viability'. If 'layout' is specified, the plate layout will be plotted in a heatmap according to the information in the 'wellType' column. If 'zscore' is chosen, the zscore of each well on a plate will be plotted in the heatmaps. If 'viability' is used, the normalized intensity or viability values on each plate will be plotted. This choice is only valid when plate normalization is performed by readScreen() function or normalizePlate() function. Default is 'layout'
ifCorrected	a logical value, whether to plot values after edge effect correction. The default value is FALSE, plot the original value.
limits	a numeric vector indicates the lower and upper limits of the value shown in the heatmap. The default values is [0,2] for plotType = "viability" and [-3,3] for plotType = 'zscore'.
pdfName	a character string specifying the output pdf file name. If not specified, a list containing the ggplot objects of plate plots will be returned. Default is NULL.
ncol	the number of columns in a pdf page. Default number is 2.
nrow	the number of rows in a pdf page. Default number is 3.
width	the width of the page, in points
height	the height of the page, in points

Value

If the argument pdfName = NULL, this function returns a list of ggplot objects and each object is a heatmap for each plate. If a file name is specified \ for the pdfName argument, a pdf file with the specified name and layout will be created in the working directory.

Examples

# load processed data
data('screenData_normalized')

# plot the cell viability heatmap on all plates
plotPlate(screenData_normalized, plotPlate = 'all', plotType = 'viability')
# Please see the vignette for more information.

lujunyan1118/DrugScreenExplorer_dev documentation built on Dec. 21, 2021, 12:42 p.m.