This package is an R wrapper around too-many-cells. See
https://github.com/GregorySchwartz/too-many-cells for latest version of the
program this wrapper targets.
See the publication (and please cite!) for more information about the algorithm.
too-many-cells is a suite of tools, algorithms, and visualizations focusing on
the relationships between cell clades. This includes new ways of clustering,
plotting, choosing differential expression comparisons, and more!
TooManyCellsR is an R wrapper around too-many-cells to facilitate
ease-of-use for R users. This package requires =too-many-cells= to be installed
and in your path! See https://github.com/GregorySchwartz/too-many-cells for
detailed installation instructions.
First install too-many-cells using the instructions in the documentation.
Next, install this packages from github:
install.packages("devtools")
library(devtools)
install_github("GregorySchwartz/tooManyCellsR")This package allows for all features from too-many-cells to be used in R, with
a focus on the make-tree entry point. For more information about the different
options, see the documentation for make-tree with included examples at
https://github.com/GregorySchwartz/too-many-cells.
The input matrix should be of Matrix format from the Matrix library, with cell
barcode column names and features (genes) as row names. The labels argument
takes a data frame with item (cell barcodes) and label (whatever labels you
want to give them, such as tissue of origin, celltype, etc.) columns.
The args argument contains a list of command line arguments fed to
too-many-cells. The default is to just have make-tree as an argument. For a
detailed list, check too-many-cells make-tree -h and check out the
documentation at https://github.com/GregorySchwartz/too-many-cells.
The main function to use is tooManyCells. For example:
tooManyCells(mat, args = c("make-tree", "--smart-cutoff", "4", "--min-size", "1"))
plot(res$treePlot, axes = FALSE)
res$stdout
res$nodeInfo
plot(res$clumpinessPlot, axes = FALSE)