plotTrProbs: Function for plotting transition probabilities between...

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Function for plotting transition probabilities between clusters

Description

This function plots the transitions probabilities in a dimensional reduction representation of a RaceID SCseq object updates with the updateSC function. in order to utilize RaceID functions for visualization.

Usage

plotTrProbs(
  object,
  probs,
  tp = 0.5,
  prthr = 0,
  cthr = 0,
  fr = FALSE,
  um = FALSE,
  cex = 0.5
)

Arguments

object	RaceID SCseq object, updated with the updateSC function.
probs	Matrix of transition probabilities between clusters, returned by the transitionProbs function.
tp	Positive real number between 0 and 1. Transparency of the data points in the dimensional reduction map. Default is 0.5.
prthr	Positive real number between 0 and 1. Threshold of transition probabilities. Only transitions with probability >prthr are displayed in the map. Default is 0.
cthr	Integer number greater or equal 0 defining the minimum clusters size for inclusion into the map. Default is 0.
fr	Logical. If TRUE, then a Fruchterman-Rheingold graph layout is shown (in case it has been computed for the RaceID bject), otherwise a t-SNE map is shown. Default is FALSE.
um	Logical. If TRUE then plot umap dimensional reduction representation. Default is FALSE.
cex	Real positive number. Size of data points. Default is 0.5.

Value

None

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
d <- getExpData(sc)
res <- pruneKnn(d,distM=sc@distances,knn=10,alpha=1,no_cores=1,FSelect=FALSE)
cl <- graphCluster(res,pvalue=0.01)
sc <- updateSC(sc,res=res,cl=cl)
sc <- comptsne(sc)
probs <-transitionProbs(res,cl,pvalue=0.01)
plotTrProbs(sc,probs,tp=.5,prthr=0,cthr=0,fr=FALSE)

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.