View source: R/FateID_functions.R
plotheatmap | R Documentation |
This function allows plotting of normalized or z-score transformed pseudo-temporal expression profiles and permits highlighting of partitioning along the x-axis and the y-axis
plotheatmap( x, xpart = NULL, xcol = NULL, xlab = TRUE, xgrid = FALSE, ypart = NULL, ycol = NULL, ylab = TRUE, ygrid = FALSE, cex = 1 )
x |
data frame with input data to show. Columns will be displayed on the x-axis and rows on the y-axis in the order given in |
xpart |
optional vector with integer values indicating partitioning of the data points along the x-axis. For instance, |
xcol |
optional vector with valid color names. The number of components has to be equal to the number of different values on |
xlab |
logical value. If |
xgrid |
logical value. If |
ypart |
optional vector with integer values indicating partitioning of the data points along the y-axis. For instance, |
ycol |
optional vector with valid color names. The number of components has to be equal to the number of different values on |
ylab |
logical value. If |
ygrid |
logical value. If |
cex |
positive real number. Size of axis labels. Default is 1. |
None
x <- intestine$x y <- intestine$y v <- intestine$v fcol <- intestine$col tar <- c(6,9,13) fb <- fateBias(x,y,tar,z=NULL,minnr=5,minnrh=10,nbfactor=5,use.dist=FALSE,seed=NULL,nbtree=NULL) dr <- compdr(x,z=NULL,m="cmd",k=2,tsne.perplexity=30) pr <- prcurve(y,fb,dr,k=2,m="cmd",trthr=0.4,start=NULL) n <- pr$trc[["t6"]] fs <- filterset(v,n,minexpr=2,minnumber=1) s1d <- getsom(fs,nb=1000,alpha=.5) ps <- procsom(s1d,corthr=.85,minsom=3) plotheatmap(ps$all.e,xpart=y[n],xcol=fcol,ypart=ps$nodes,xgrid=FALSE,ygrid=TRUE,xlab=FALSE)
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