【slingshot】trajectory inference

condiments Paper • condimentsPaper

First example: TGF-beta dataset • bioc2021trajectories

 

slingshot requires a minimum of two inputs: (1)a matrix representing the cells in a reduced-dimensional space. (2)a vector of cluster labels.

主要步骤：

（1）getLineages function to identify global lineage structrue by construsting MST on the clusters

（2）getCurves function to construct smooth curves and infer the psudotime variable

• simulated dataset 1 (single trajectory) and dataset 2 (bifurcating)

#####dataset1
# generate synthetic count data representing a single lineage
means <- rbind(
    # non-DE genes
    matrix(rep(rep(c(0.1,0.5,1,2,3), each = 300),100),
        ncol = 300, byrow = TRUE),
    # early deactivation
    matrix(rep(exp(atan( ((300:1)-200)/50 )),50), ncol = 300, byrow = TRUE),
    # late deactivation
    matrix(rep(exp(atan( ((300:1)-100)/50 )),50), ncol = 300, byrow = TRUE),
    # early activation
    matrix(rep(exp(atan( ((1:300)-100)/50 )),50), ncol = 300, byrow = TRUE),
    # late activation
    matrix(rep(exp(atan( ((1:300)-200)/50 )),50), ncol = 300, byrow = TRUE),
    # transient
    matrix(rep(exp(atan( c((1:100)/33, rep(3,100), (100:1)/33) )),50), 
        ncol = 300, byrow = TRUE)
)
counts <- apply(means,2,function(cell_means){
    total <- rnbinom(1, mu = 7500, size = 4)
    rmultinom(1, total, cell_means)
})
rownames(counts) <- paste0('G',1:750)
colnames(counts) <- paste0('c',1:300)
sce <- SingleCellExperiment(assays = List(counts = counts))


#####dataset2
library(slingshot, quietly = FALSE)
data("slingshotExample")
rd <- slingshotExample$rd
cl <- slingshotExample$cl

dim(rd) # data representing cells in a r