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Last data update: 2014.03.03

R: Plot fitted bivariate normal distribution.

plotNorm2

R Documentation

Plot fitted bivariate normal distribution.

Description

Plots objects derived from function fitNorm2 in false color represenation.

Usage

plotNorm2(fn, colrange=c("gray82", "blue"), center=TRUE, selection=FALSE,
                      ellipse=FALSE, pch=20, cex=1, col="dens", ...)

Arguments

`fn`	List. Object derived from function `fitNorm2`
`colrange`	Character vector with valid color identifiers (eg name or RGB values) from which a smooth color palette is derived.
`center`	Logical. Assign center of distribution.
`selection`	Logical. Mark all points beyond selection.
`ellipse`	Logical. Plot area and borders of selection as ellipse.
`pch`	see `par`
`cex`	see `par`
`col`	see `par` or special cases `dens` for coloring according to density and `prob` for coloring according to probability.
`...`	further arguments that are passed on to `plot`.

Details

Produces a scatterplot of paired data showing the densities of the fitted bivariate distribution from function fitNorm2 in false color representation. Additionally a selection of data points can be highlighted either by marking outliers or by showing its area.

Value

A list containing items p, cov, mu, S (density values for each data pair, resulting object from call to cov.rob, midpoint of distribution, covariance matrix).

Author(s)

Florian Hahne

Examples

 sampdat <- readFCS(system.file("extdata",
   "fas-Bcl2-plate323-04-04.A01", package="prada"))
 nfit   <- fitNorm2(exprs(sampdat[,1:2]), scalefac=2)
 plotNorm2(nfit, selection=TRUE, ellipse=TRUE)

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)

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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(prada)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase

Attaching package: 'robustbase'

The following object is masked from 'package:Biobase':

    rowMedians

Scalable Robust Estimators with High Breakdown Point (version 1.3-11)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/prada/plotNorm2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotNorm2
> ### Title: Plot fitted bivariate normal distribution.
> ### Aliases: plotNorm2
> 
> ### ** Examples
> 
>  sampdat <- readFCS(system.file("extdata",
+    "fas-Bcl2-plate323-04-04.A01", package="prada"))
>  nfit   <- fitNorm2(exprs(sampdat[,1:2]), scalefac=2)
>  plotNorm2(nfit, selection=TRUE, ellipse=TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>