spatialDistribHits: Plotting the spatial distribution of the hits
In RNAither: Statistical analysis of high-throughput RNAi screens

Description Usage Arguments Value See Also Examples

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

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

`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.

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

Ttest

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)