## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, results = 'hide') library(veloviz) ## ----eval = FALSE------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("veloviz") # ## ----------------------------------------------------------------------------- data(vel) curr <- vel$current #observed current transcriptional state proj <- vel$projected #predicted future transcriptional state ## ----------------------------------------------------------------------------- veloviz <- veloviz::buildVeloviz(curr = curr, proj = proj, normalize.depth = TRUE, use.ods.genes = FALSE, pca = TRUE, nPCs = 3, center = TRUE, scale = TRUE, k = 10, similarity.threshold = -1, distance.weight = 1, distance.threshold = 1, weighted = TRUE, verbose = FALSE) ## ----------------------------------------------------------------------------- emb.veloviz <- veloviz$fdg_coords plot(emb.veloviz) ## ----------------------------------------------------------------------------- sessionInfo()