CFMexplorer: Shiny app for interactive visualization of expression...

In vjcitn/fatemapper: tools for working with cell fate maps

Description

Shiny app for interactive visualization of expression patterns related to cell fate map

Usage

CFMexplorer()

Note

A spatial expression matrix has rows corresponding to a mapping of a grid, and columns corresponding to a gene; see data(expressionPatterns) for an example. A reexpression of such a matrix using non-negative matrix factorization is described in Wu et al., PNAS, 2016 http://www.pnas.org/content/113/16/4290.full. The basis matrix of this factorization yields what Wu et al. call 'principal patterns'. To visualize these patterns in the context of the cell fate map, we take the convex hulls of points having pattern weights exceeding a given threshold. There are three different basis sets offered: Wu's distribution through supplemental data for the PNAS paper, a direct computation of a rank 21 NMF from the expressionPatterns, and a direct computation of a rank 30 NMF from the same data.

vjcitn/fatemapper documentation built on May 3, 2019, 6:14 p.m.