lineage is an R package to help infer lineage graph from single cell transcriptomic
data where a pseudotime and a celltype score matrix is available.
devtools::install_github("BioinfoSupport/lineage")library(lineage)
set.seed(123)
pseudotime <- runif(1000)
identity_scores <- matrix(runif(10000),1000,dimnames=list(NULL,LETTERS[1:10]))
g <- lineage_graph_build(pseudotime,identity_scores)
plot_lineage_graph(g)
plot_lineage_incidence_matrix(g,pseudotime,identity_scores)
plot_lineage_incidence_matrix(g)
g <- lineage_graph_prune(g)
plot_lineage_graph(g)
lineage_coords(g,pseudotime,identity_scores) %>% ggplot() + geom_jitter(aes(x=pseudotime,y=lineage_label,color=identity_label))
lineage_coords(g,pseudotime,identity_scores) %>% ggplot() + ggridges::geom_density_ridges(aes(x=pseudotime,y=lineage_label,fill=identity_label),alpha=0.5)