tooManyCellsR

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#+TITLE: tooManyCellsR #+AUTHOR: Gregory W. Schwartz #+OPTIONS: date:nil creator:nil timestamp:nil toc:t

#+SETUPFILE: https://fniessen.github.io/org-html-themes/setup/theme-readtheorg.setup

[[https://gregoryschwartz.github.io/too-many-cells/][Website]]

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 [[https://doi.org/10.1038/s41592-020-0748-5][the publication]] (and please cite!) for more information about the algorithm.

[[file:img/pruned_tree.png]]

• Description

=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.

• Installation

First install =too-many-cells= using the instructions in the [[https://github.com/GregorySchwartz/too-many-cells][documentation]]. Next, install this packages from github:

#+BEGIN_SRC R install.packages("devtools") library(devtools) install_github("GregorySchwartz/tooManyCellsR") #+END_SRC shell

• Usage

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:

#+BEGIN_SRC R 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) #+END_SRC r