inst/doc/roots.R

In roots: Reconstructing Ordered Ontogenic Trajectories

## ----installation, echo=TRUE, eval=FALSE---------------------------------
#  library(devtools)
#  install_github("wjawaid/roots")

## ----example, echo=TRUE, eval=FALSE--------------------------------------
#  library(roots)
#  
#  ## Load data
#  blood <- read.table("http://blood.stemcells.cam.ac.uk/data/norm_counts_nestorowa_data.txt", sep = " ")
#  cellNames <- read.table("http://blood.stemcells.cam.ac.uk/data/cell_names_nestorowa_data.txt", sep = " ", stringsAsFactors = FALSE)[,1]
#  rownames(blood) <- gsub("LT\\.", "LT-", cellNames)
#  geneNames <- read.table("http://blood.stemcells.cam.ac.uk/data/gene_names_nestorowa_data.txt", sep = " ", stringsAsFactors = FALSE)[,1]
#  colnames(blood) <- geneNames
#  blood <- as.matrix(blood)
#  rm(cellNames, geneNames)
#  
#  ## Load metadata
#  meta <- read.csv("http://blood.stemcells.cam.ac.uk/data/wj_out_jd.csv")
#  colnames(meta) <- c("cellType", "index", "name")
#  rownames(meta) <- meta$name
#  meta$col <- bglab::ggCol(meta$cellType)
#  nmeta <- data.frame(col=rep("#00000011", nrow(blood)), stringsAsFactors = FALSE, row.names = rownames(blood))
#  nmeta[rownames(meta),"col"] <- meta$col
#  leg <- data.frame(cell=as.character(unique(meta$cellType)), col=as.character(unique(meta$col)), stringsAsFactors = FALSE)
#  legOrd <- c(5, 8, 6, 7, 1, 4, 2, 3)
#  
#  ## Analyse
#  xx <- goggles(blood)
#  
#  ## Plot
#  plot(xx$l, pch=16, col = nmeta[rownames(xx$l), "col"])
#  legend("topright", legend = leg$cell[legOrd], fill=leg$col[legOrd], inset=0.02)
#