displayPlate: Draw a summary display for a GeneTitan plate...
In titanQC: QC Procedures for the GeneTitan platform

Description Usage Arguments Value Note

View source: R/displayPlate.R

Draw a summary display for a GeneTitan plate

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displayPlate(eset, statistic, type="GeneTitan", stepSize=0.01, main, legend, breaks,
    text, textsize=0.7, textcol="black", color="heat",
    filePrefix="displayPlate")

`eset`	ExpressionSet object with additional plate number and position information in the pData; for the Incubator plates (cf. note) the column names of the pData need to be incubatorPlateNo, incubatorColumn, incubatorRow; for GeneTitan plates the column names of the pData need to be titanPlateNo, titanColumn, titanRow
`statistic`	summary statistic or information to be displayed for a well on the plate; can be either a name of a pData variable or a vector of values (one for each well) respecting the row order of pData variables
`type`	type of plate; one of 'GeneTitan' (default) or 'Incubator'
`stepSize`	step size used to discretize the range of summary values to be displayed; the step size is reflected in the distance between ticks on the heatmap legend and each step is associated with a different color level in the heatmap
`main`	main title for the plot; if NULL (default) 'Plate n' is used where n is the plate number; if only one plate is present no title is displayed; if the user provides a main title (string) and there is more than one plate present, the plate numbers are added to the title between round brackets, as in 'Main Title (Plate n)'.
`legend`	title of the legend (character of length one); if NULL (default) no legend is drawn
`breaks`	vector of break points supplied to the image function; if NULL (default) the break points are generated automatically
`text`	name of a pData variable to be displayed; each cell of the plate grid will be annotated using the value in the corresponding pData variable
`textsize`	cex argument to be passed to the text function which will display the values specified in the 'text' argument
`textcol`	col argument to be passed to the text function which will display the values specified in the 'text' argument
`color`	color scheme to be used for the cells of the grid; if 'heat' heat colors are used, if 'redgreen' the colors go from green (low) to black (medium) to red (high); if 'random' rainbow colors are used (typically used for discrete variables), if 'white' the background color of the cells is 'white'; alternatively the name of a pData variable can be passed and will be used to set the colors of the cells; for any color scheme all missing values are set to 'black'
`filePrefix`	prefix used for all pdf files; one pdf file is generated for each plate; defaults to "displayPlate"

no return value; one pdf file is generated for each plate

If the profiled samples originate from an in vitro experiment, the information of the cell culture plates (Incubator plates) can be added to the pData of the ExpressionSet object

titanQC documentation built on May 2, 2019, 5:55 p.m.