plotexpression: Plotting of pseudo-temporal expression profiles

In dynverse/StemID2: De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

Description

This function allows plotting pseudo-temporal expression profiles for single genes or groups of genes.

Usage

plotexpression(x, y, g, n, col = NULL, name = NULL, cluster = FALSE,
  k = 5, locreg = FALSE, alpha = 0.5, types = 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. In the latter case, the input argument x needs to be provided. A vector of gene IDs can also be provided. In this case, the aggregated expression across all gene IDs is plotted.
n	ordered vector of cell IDs to be included. Cell IDs need to be column names of x.
col	optional vector of valid color names for all clusters in y ordered by increasing cluster number. 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.
k	positive integer number. Pseudo-temporal expression profiles are either derived using a running mean of expression values across the ordered cells with window-size k, or by a local regression (if locreg is TRUE). Default value is 5.
locreg	logical value. If TRUE, then 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. Default value is TRUE.
alpha	positive real number. This is the parameter, which controls the degree of smoothing. Larger values return smoother profiles. Default value is 0.5.
types	optional vector with IDs for different subsets of cells in y, e. g. different batches. All cells with the same ID will be displayed by the same symbol and color. Default value is NULL

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)
trc <- dptTraj(x,y,fb,trthr=.25,distance="euclidean",sigma=1000)
n <- trc[["t6"]]
fs  <- filterset(v,n,minexpr=2,minnumber=1)
s1d <- getsom(fs,nb=1000,k=5,locreg=TRUE,alpha=.5)
ps <- procsom(s1d,corthr=.85,minsom=3)
# plot average profile of all genes of node 1 in the self-organizing map
g <- names(ps$nodes)[ps$nodes == 1]
plotexpression(v,y,g,n,k=25,col=fcol,name="Node 1",cluster=FALSE,locreg=TRUE,alpha=.5,types=NULL)

dynverse/StemID2 documentation built on May 25, 2019, 4:25 p.m.