plotexpressionProfile: Plotting smoothed pseudo-temporal expression profiles for...

In dgrun/FateID: Quantification of Fate Bias in Multipotent Progenitors

Plotting smoothed pseudo-temporal expression profiles for groups of genes

Description

This function allows plotting loess-smoothed pseudo-temporal expression profiles for groups of genes. To display gene expression profiles on the same scale, row sums are normalized to one.

Usage

plotexpressionProfile(
  x,
  y,
  g,
  n,
  logsc = FALSE,
  col = NULL,
  name = NULL,
  cluster = FALSE,
  alpha = 0.5,
  lwd = 1,
  ylim = NULL,
  seed = 12345,
  ylab = NULL
)

Arguments

x	expression data frame with genes as rows and cells as columns. Gene IDs should be given as row names and cell IDs should be given as column names.
y	clustering partition. A vector with an integer cluster number for each cell. The order of the cells has to be the same as for the columns of x.
g	a gene ID corresponding to one of the rownames of x. It can also be vector of gene IDs. In this case, a separate profile is plotted for each gene in g.
n	ordered vector of cell IDs to be included. Cell IDs need to be column names of x.
logsc	logical value. If TRUE, then log2-transformed values are plotted. Default is FALSE and untransformed values are plotted.
col	optional vector of valid color names used for the profiles of all genes in g. Default value is NULL.
name	optional character string. This argument corresponds to a title for the plot. Default value is NULL. If not provided, and g is given, then name will equal g or g[1], respectively, if g is a vector of gene IDs.
cluster	logical value. If TRUE then the partitioning along the x-axis is indicated be vertical lines representing the boundaries of all positions with a given value in y. The average position across all cells in a cluster will be indicated on the x-axis.
alpha	positive real number. Pseudo-temporal expression profiles are derived by a local regression of expression values across the ordered cells using the function loess from the package stats. This is the parameter, which controls the degree of smoothing. Larger values return smoother profiles. Default value is 0.5.
lwd	line width of profiles. Default value is 1.
ylim	vector of two numerical values: lower and upper limit of values shown on the y-axis. Default value is NULL and the whole range is shown.
seed	integer number. Random seed for determining colour scheme. Default is 12345.
ylab	Optional label for the y-axis. Default is NULL and axis is labeled "norm. expression".

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$trc[["t6"]]
fs  <- filterset(v,n,minexpr=2,minnumber=1)
s1d <- getsom(fs,nb=1000,alpha=.5)
ps <- procsom(s1d,corthr=.85,minsom=3)
# plot average profile of all genes of node 1 in the self-organizing map
g <- sample(names(ps$nodes)[ps$nodes == 1],5)
plotexpressionProfile(v,y,g,n,col=fcol,name="Node 1",alpha=.2)

dgrun/FateID documentation built on June 20, 2022, 12:57 p.m.