Generate Weights

Description

Because the manta plot uses integer count data, many of the points overlap and hide a large portion of the data. This function allows one to apply a weighting scheme to jitter points out from under each other both to show the density and expose the content of their pies (if applicable).

Usage

generateWeights(x, w.clmn,  agg.clmn, cond.clmn, ct.clmns=NULL)

Arguments

Value

a 2 by n weight matrix

See Also

manta

Examples

align.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.tab", package="manta")
a <- read.delim(align.path, stringsAsFactors=FALSE)
w <- generateWeights(a, 'what_e_value', 'what_def', 'treatment')

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.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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(manta)
Loading required package: edgeR
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/manta/generateWeights.Rd_%03d_medium.png", width=480, height=480)
> ### Name: generateWeights
> ### Title: Generate Weights
> ### Aliases: generateWeights
> 
> ### ** Examples
> 
> align.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.tab", package="manta")
> a <- read.delim(align.path, stringsAsFactors=FALSE)
> w <- generateWeights(a, 'what_e_value', 'what_def', 'treatment')
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>