Nothing
abundancePlot <- function (res.list, log = FALSE, printLimit = 16, Group=NULL, Plot=FALSE,
CountCutOff=3, ...)
{
abundance.list <- lapply(res.list, FUN = function(v) {
v$abundance
})
counts.list <- lapply(res.list, FUN = function(v) {
v$counts[, 1]
})
abundance <- sapply(res.list, FUN = function(v) {
v$abundance
})
fnames <- sapply(res.list, FUN = function(v) {
v$fname
})
colnames(abundance) <- fnames
IDlist <- colnames(res.list[[1]]$abundance)
# DP 2012-05-24
# modify to allow for random lists, not just GO
if (length(grep("^GO:", IDlist)) == length(IDlist)) {
#GOIDlist = gsub(";", "", GOIDlist)
Terms <- sapply(IDlist, FUN = function(v) { Term(GOTERM[[v]]) } )
#jw 11/11/19
IDlist <- Terms
} else {
Terms <- IDlist
}
nFiles <- rownames(res.list[[1]]$abundance)
Source <- rep(nFiles, length(IDlist))
Term <- rep(Terms, each = length(nFiles))
rownames(abundance) <- paste(Source, Term)
Value <- as.vector(abundance)
if (log) Value <- log(Value + eps);
GG <- rep(Term, ncol(abundance))
SS <- rep(Source, ncol(abundance))
FF <- rep(gsub(".*\\/", "", colnames(abundance)), each = nrow(abundance))
#
list.barplots <- list()
if(Plot) {
for (gg in unique(GG)[seq_len(min(length(unique(GG)),printLimit)) ] ) {
# #JW
list.barplots[[gg]] <- barchart(Value ~ GG | FF, groups = SS, , main = gg,
scales = list(x = list(rot = 45)), auto.key = list(points = FALSE,
rectangles = TRUE, space = "top"), subset = (GG ==
gg))
}
}
# Only plot counts >= CountCutOff
list.levelplots <- list()
for (i in seq_along(fnames)) {
nzero = sum(!(counts.list[[i]]==0))
idx2plot = counts.list[[i]] >= CountCutOff
if(sum(idx2plot) > 2) {
# png(paste("File", i, ".png", sep = ""), 2000, 4000, res = 200)
list.levelplots[[fnames[i]]] <- plotMat(abundance.list[[i]][,idx2plot], counts.list[[i]][idx2plot],
main = paste("Abundance levelplot",
fnames[i]))
# dev.off()
}
}
ag.mat <- NULL
if (!is.null(Group)) {
ag.list <- aggregateAbundance(res.list, Group=Group)
#
# should review this part; DP Nov 2019
# remove
x <- extractPairs(res.list, ag.list, fnames[1:2], Group[1])
# png("CountAndAbundance.png", 2000, 2000, res=300)
# countAndAbundance(x, legend.text=fnames[1:2])
# dev.off()
ag.mat <- ag.list[[1]]
for (jj in 2:length(ag.list)) ag.mat <- rbind(ag.mat, ag.list[[jj]]);
Files <- as.factor(rep(fnames, each=nlevels(as.factor(Group))))
rownames(ag.mat) <- paste(rownames(ag.mat), Files)
#write.csv(ag.mat, file="AggregateAbundanceMat.csv")
}
# abundance
list(abundance=abundance, ag.mat=ag.mat, list.levelplots=list.levelplots, list.barplots=list.barplots)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.