view.aspects

row.clustering

cell.clustering

Range of the normalized gene expression levels, inputted as a list: c(lower_bound, upper_bound). Values outside this range will be Winsorized. Useful for increasing the contrast of the heatmap visualizations. Default, set to the 5th and 95th percentiles.

zlim

row.cols

Matrix of column colors. Useful for visualizing cell annotations such as batch labels.

col.cols

cols

Boolean of whether to show row variance as a color track

show.row.var.colors

Restrict output to the top n aspects of heterogeneity

additional arguments for heatmap plotting


Internal function to visualize aspects of transcriptional heterogeneity as a heatmap. Used by <code><a rd-options="" href="/link/pagoda.view.aspects?package=scde&version=2.0.0" data-mini-rdoc="scde::pagoda.view.aspects">pagoda.view.aspects</a></code>.


The scde package implements a set of statistical methods for
analyzing single-cell RNA-seq data. scde fits individual error models for
single-cell RNA-seq measurements. These models can then be used for assessment
of differential expression between groups of cells, as well as other types of
analysis. The scde package also contains the pagoda framework which applies
pathway and gene set overdispersion analysis to identify and characterize
putative cell subpopulations based on transcriptional signatures. The overall
approach to the differential expression analysis is detailed in the following
publication: "Bayesian approach to single-cell differential expression
analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi:
10.1038/nmeth.2967). The overall approach to subpopulation identification and
characterization is detailed in the following pre-print: "Characterizing
transcriptional heterogeneity through pathway and gene set overdispersion
analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F,
Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).

Peter Kharchenko

scde

Single Cell Differential Expression

view.aspects function


Internal function to visualize aspects of transcriptional heterogeneity as a heatmap. Used by <code><a rd-options='' href='pagoda.view.aspects'>pagoda.view.aspects</a></code>.


view.aspects: View heatmap

Description

Usage

Arguments

Value