plotheatmap {FateID}

Heatmap of expression profiles

Description

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

Usage

plotheatmap(
  x,
  xpart = NULL,
  xcol = NULL,
  xlab = TRUE,
  xgrid = FALSE,
  ypart = NULL,
  ycol = NULL,
  ylab = TRUE,
  ygrid = FALSE,
  cex = 1
)

Arguments

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 x. For example, columns can correspond to cells in pseudo-temporal order and rows contain gene expression, i. e. rows can represent pseudo-temporal gene expression profiles.

xpart

optional vector with integer values indicating partitioning of the data points along the x-axis. For instance, xpart can be a cluster assignment of cell IDs. The order of the components has to be the same as for the columns in x. Default value is NULL.

xcol

optional vector with valid color names. The number of components has to be equal to the number of different values on xpart. If provided, these colors are used to highlight partitioning along the x-axis based on xpart. Default value is NULL.

xlab

logical value. If TRUE then the average position is indicated for each partition value along the x-axis. Default value is TRUE.

xgrid

logical value. If TRUE then the partitioning along the x-axis is indicated by vertical lines representing the boundaries of all positions with a given value in xpart.

ypart

optional vector with integer values indicating partitioning of the data points along the y-axis. For instance, ypart can be the assignment of gene IDs to nodes of a sel-organizing map. The order of the components has to be the same as for the rows in x. Default value is NULL.

ycol

optional vector with valid color names. The number of components has to be equal to the number of different values on ypart. If provided, these colors are used to highlight partitioning along the y-axis based on ypart. Default value is NULL.

ylab

logical value. If TRUE then the average position is indicated for each partition value along the y-axis. Default value is TRUE.

ygrid

logical value. If TRUE then the partitioning along the y-axis is indicated by horizontal lines representing the boundaries of all positions with a given value in ypart.

cex

positive real number. Size of axis labels. Default is 1.

Value

None

Examples

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)