Reconstructing Ordered Ontogenic Trajectories

A set of tools to reconstruct ordered ontogenic trajectories from single cell RNAseq data.


Wajid Jawaid 2017-07-09

Project Status: Active - The project has reached a stable, usable state and is being actively developed.

Reconstructing ordered ontogenic trajectories provides methods for:

  1. Identifying informative genes (crude),
  2. Finding a sparse graph structure between closely related cells by removing spurious edges and
  3. Traversing the graph in a biologiclal informed way using a Directed Non-markovian Monte-Carlo method.

The main goal of roots is to infer plausible developmental journeys guided by the user.

Installation

library(devtools)
install_github("wjawaid/roots")

Example

Here I take the mouse adult haematopoietic data from Nestorowa et al.. Data is downloaded and processed using the goggles() function as below.

library(roots)
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)

Output from goggle() function

News

Reference manual

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install.packages("roots")

1.0 by Wajid Jawaid, 2 years ago


Browse source code at https://github.com/cran/roots


Authors: Wajid Jawaid [aut, cre]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports animation, rARPACK, igraph

Suggests knitr, rmarkdown


See at CRAN