plotdesign: Field map of RNA-seq experimental design

In Lina-Gao/DEdesign: Statistical design for RNA-seq experiments aimed at identifying differentially expressed genes

Description

Plot the RNA-seq experimental design in the format of Illumina 8-lane flow cell

Usage

plotdesign(x, selection)

Arguments

x	a DEdesign object (output from gendesign) or a data.frame containing flowcell, lane and adapter assignment can also be plotted. It should have 4 columns with column names flowcell, lane, adapter, treatment. flowcell, lane, adapter should be integer values starting from 1; character values are expected for treatment.
selection	If x is a DEdesign object, select which design to plot: "Design" based on input or "suggestedDesign". Default is "Design".

Value

a ggplot2 object

Examples

treatments <- data.frame(trt = letters[1:6], replicates = rep(3,6))
des <- gendesign(treatments=treatments, nperlane=4, search.surrounding = 2)
plotdesign (des,selection="Design")
plotdesign (des,selection="suggestedDesign")
plotdesign (des$suggestedDesign$design)

Lina-Gao/DEdesign documentation built on May 5, 2019, 2:39 a.m.