spatialDistribHits {RNAither} | R Documentation

## 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)

[Package RNAither version 2.28.0 Index]