RNAither (version 2.20.0)

spatialDistribHits: Plotting the spatial distribution of the hits

Description

Plots the plates showing the spatial distribution of the hits using the plotPlate function of the prada package.

Usage

spatialDistribHits(header, dataset, plotTitle, col4hits, col4anno, showPlot)

Arguments

header

the header of a dataset file generated with generateDatasetFile

dataset

an R data frame generated with generateDatasetFile

plotTitle

the plot title

col4hits

a character vector specifying the name of the dataset column containing the binary hit vector

col4anno

a character string specifying the name of the dataset column to be used to define the replicate, e.g. "GeneName" or "Internal_GeneID"

showPlot

0 or 1. 1 will open one or several plot windows in the R GUI, 0 will only save the plot(s) without opening windows.

Value

For each plate, the plot will be saved as a png file named after the experiment name specified in the header concatenated with the plotTitle, the number of the experiment, and the number of the plate.Wells containing positive controls are marked with a "P", wells containing negative controls with an "N".Each plate will also be saved as an html file containing mouse-overs with the siRNA name for each well.The function returns a list containing:

histoName

the plotname

c(minOfScreens, numOfScreens)

a vector with the number of the first experiment and of the last experiment

c(minOfPlates, numOfPlates)

a vector with the number of the first plate and the number of the last plate

See Also

Ttest

Examples

data(exampleHeader, package="RNAither")
data(pValVec1, package="RNAither")
data(scoredDataset1, package="RNAither")

##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above.

scoredHits1 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "Hits1", 0.05, 
"GeneName", "pvalue_testfile1.txt")

hitDataset1 <- scoredHits1[[1]]

spatialDistribHits(header, hitDataset1, "Spatial distribution of hits", "Hits1", "GeneName", 1)