group_map: model color map

In RNAdecay: Maximum Likelihood Decay Modeling of RNA Degradation Data

Description

group_map makes a color map of alpha and beta equivalence groups by model. Similar colors in a row indicate constrained parameter equivalence between treatements. Gray indicates values of 0.

Usage

group_map(decaydata, path, nEquivGrp = nEquivGrp, groups = groups, mods = mods)

Arguments

decaydata	5 column data.frame with colnames "geneID","treatment","t.decay","rep","value"
path	write path and file name, must end in ".pdf"
nEquivGrp	number of equivalence groups based on number of treatments
groups	equivalence group matrix
mods	alpha beta equivalence group usage index (matrix)

Value

creates a model colormap and writes it to a pdf file named path

Examples

group_map(decaydata=data.frame(geneID=paste0("gene",1:4),
                    treatment=as.factor(rep(paste0("treat",1:2),2)),
                    t.decay=0:3,
                    rep=rep("rep1"),
                    value=c(1,0.5,0.25,0.12)),
         path=paste0(tempdir(),"/parameter equivalence colormap.pdf"),
         nEquivGrp = 2,
         groups = t(matrix(c(1,2,1,1,NA,NA),nrow=2,
                    dimnames=list(c("treat1","treat2"),c("grp1","grp2","grp3")))),
         mods = t(matrix(c(1,1,1,2,1,3,2,1,2,2,2,3),nrow=2,
                         dimnames=list(c("a","b"),paste0("mod",1:6)))))

RNAdecay documentation built on Nov. 8, 2020, 5:52 p.m.