Last data update: 2014.03.03

R: Plot Z by TF out-degree quantiles
plotZbyTFR Documentation

Plot Z by TF out-degree quantiles

Description

Generates a Z-score scatterplot for edges according to the TF outdegree in prior. The two PANDA objects should only differ in the gene expression used for the network constructions or other parameters.

Usage

plotZbyTF(x, y, motif, hasPrior = TRUE, cuts = 1, cols = 2)

Arguments

x

PANDA object - output of the panda function.

y

PANDA object - second PANDA object.

motif

Motif used to construct the networks.

hasPrior

TRUE/FALSE, If TRUE plots the edges that are given a weight > 0 in the motif, else plot those given a weight of 0

cuts

either a numeric vector of two or more unique cut points or a single number (greater than or equal to 2) giving the number of intervals into which 'x' is to be cut.

cols

Number of columns in layout.

Value

ggplot heatmapfor each TF, get outdegree in regulatory prior

Examples

data(pandaResult)
data(pandaToyData)
plotZbyTF(pandaResult,pandaResult, pandaToyData$motif, hasPrior=TRUE)
plotZbyTF(pandaResult,pandaResult, pandaToyData$motif, cuts=2)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(pandaR)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pandaR/plotZbyTF.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotZbyTF
> ### Title: Plot Z by TF out-degree quantiles
> ### Aliases: plotZbyTF
> 
> ### ** Examples
> 
> data(pandaResult)
> data(pandaToyData)
> plotZbyTF(pandaResult,pandaResult, pandaToyData$motif, hasPrior=TRUE)
> plotZbyTF(pandaResult,pandaResult, pandaToyData$motif, cuts=2)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>