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November 1, 2011 20:49
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Nestedness Code
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############################################################################ | |
#CODE FOR ANALYZING NESTEDNESS OF A COMMUNITY MATRIX & PLOTTING THE RESULTS# | |
############################################################################ | |
require(vegan) | |
require(ade4) | |
#Here, samp_85 is simply a community matrix of my 85% OTU cyano bins. The [5:9] just chooses | |
#specific rows for analysis (here, a depth gradient). | |
samp <- samp_85[c(5:9),] | |
sums <- subset(colSums(samp), colSums(samp) > 0) | |
samp <- samp[,names(sums)] | |
#Here's the code to calculate the NODF value for nestedness. It then compares | |
#this value to simulated values after shuffling. The "quasiswap" method is the most conservative | |
nf <- oecosimu(samp,nestednodf, method = "quasiswap", nsimul = 999, order = FALSE, weighted = FALSE) | |
nf | |
#This gives another, less informative measure of nestedness called "temperature | |
#its main benefit is that it makes a nice graph of the packed matrix, which is all I use it for | |
out <- nestedtemp(samp, order = FALSE) | |
#This does the same thing but for the amplicon libraries from the other cyano mat sections | |
samp <- samp_[c(4,10,1,11,12),] | |
sums <- subset(colSums(samp), colSums(samp) > 0) | |
samp <- samp[,names(sums)] | |
nf <- oecosimu(samp,nestednodf, method = "quasiswap", nsimul = 999, order = FALSE, weighted = FALSE) | |
nf | |
out1 <- nestedtemp(samp, order = FALSE) | |
## Finally, we can plot the packed matrix. Keep in mind that I have changed the row and | |
#column names for aesthetics, but you should simply start with plot(out, kind = "incid") | |
layout(1:2) | |
plot(out, kind="incid", col=rev(c("grey35", "white")), names = FALSE, adj = 1) | |
axis(2, at=seq(1,0,length.out = nrow(samp)), labels = rownames(samp), tick = FALSE, cex.axis = 0.75) | |
axis(3, at=seq(0,1,length.out = ncol(samp)), labels = seq(1,ncol(samp)), cex.axis = 0.75 , padj = 1, tick = FALSE) | |
title(main="Cyano OTUs (97%)\n New Mat", cex.main = 0.9, sub = "p = 0.9", cex.sub = 1, line = 2) | |
plot(out1, kind="incid", col=rev(c("grey35", "white")), names = FALSE, adj = 1) | |
axis(2, at=seq(1,0,length.out = nrow(samp)), labels = rownames(samp), tick = FALSE, cex.axis = 0.75) | |
axis(3, at=seq(0,1,length.out = ncol(samp)), labels = seq(1,ncol(samp)), cex.axis = 0.75 , padj = 1, tick = FALSE) | |
title(main="Cyano OTUs (97%)\n Old Mat", cex.main = 0.9, sub = "p = 0.30", cex.sub = 1, line = 2) |
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