I am using the code from Human vs. Chimp Brain paper https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/HumanChimp/HumanChimpNetworkAnalysis.pdf
and I have troubles with the hclustplot1 which should result from this part of code:
par(mfrow=c(2,2),mar=c(2,2,2,2)) plot(hierTOMHuman,main="WT hippocampus",labels=F) abline(h=.95,col="red") plot(hierTOMChimp,main="N3-/- hippocampus",labels=F) hclustplot1(hierTOMHuman,colorh1,title1="WT network, WT colors") hclustplot1(hierTOMChimp,colorh1,title1="N3-/- network, WT colors") colorh=as.character(colorh1) colorhALL=rep("grey", length(ConnectivityChimp)) colorhALL[rest1]=as.character(colorh)
My plot is not showing the colors in either Human or Chimp, there is just empty space under the titles.... The first (main) titles and dendrograms are plotted ok, next the titles are ok but nothing happens when the colors should show. Is there a bug in this code or am I doing something wrong?
The next plot is also not wroking well but I assume the error I get is related to memory not to the code itself (?)
TOMplot1(distTOMHuman, hierTOMHuman , colorh)
Error: C stack usage 7955296 is too close to the limit
Beside the error, it looks like the resulting plot is not ok as well - the colors are not aligned which looks very weird: