Plate plot with the row and column offsets estimated by the B score method

Description

The function plots the per-plate row and column effects estimated by the B score method.

Usage

plotSpatialEffects(x, whichChannel = 1, plateRange)

Arguments

Details

The function plots the plate plots displaying the row and column offsets (stored in slot rowcol.effects of the cellHTS object x) within the plates in plateRange, and for channel whichChannel, as determined by the B score method. Before plotting the spatial offsets, the values within the chosen channel (whichChannel) are transformed in order to be confined in the range [0, 1], as follows:

yt = (y - min(y))/(max(y) - min(y))

Here, yt are the transformed values, and y the estimated spatial effects. The maximum and the minimum values are calculated using all of the values in x$rowcol.effects[,,,whichChannel].

Author(s)

Ligia P. Bras ligia@ebi.ac.uk

See Also

plotPlate, Bscore, normalizePlates, summarizeChannels

Examples

    data(KcViabSmall)
    x = normalizePlates(KcViabSmall, normalizationMethod="Bscore",
                        save.model = TRUE)
    ## see plate plots with the row and column estimated offsets for
    ## plates 1 and 3: 
    plotSpatialEffects(x, plateRange=c(1,3))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cellHTS)
Loading required package: grid
Warning message:
Package 'cellHTS' is deprecated and will be removed from Bioconductor
  version 3.4. Please consider using 'cellHTS2' which offers better
  functionality for working with multiple screens and with
  multi-channel screens. 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cellHTS/plotSpatialEffects.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotSpatialEffects
> ### Title: Plate plot with the row and column offsets estimated by the B
> ###   score method
> ### Aliases: plotSpatialEffects
> ### Keywords: manip
> 
> ### ** Examples
> 
>     data(KcViabSmall)
>     x = normalizePlates(KcViabSmall, normalizationMethod="Bscore",
+                         save.model = TRUE)
>     ## see plate plots with the row and column estimated offsets for
>     ## plates 1 and 3: 
>     plotSpatialEffects(x, plateRange=c(1,3))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>