make.pagoda.app: Make the PAGODA app

In hms-dbmi/scde: Single Cell Differential Expression

Make the PAGODA app

Description

Create an interactive user interface to explore output of PAGODA.

Usage

make.pagoda.app(tamr, tam, varinfo, env, pwpca, clpca = NULL,
  col.cols = NULL, cell.clustering = NULL, row.clustering = NULL,
  title = "pathway clustering", zlim = c(-1, 1) * quantile(tamr$xv, p =
  0.95))

Arguments

tamr	Combined pathways that show similar expression patterns. Output of pagoda.reduce.redundancy
tam	Combined pathways that are driven by the same gene sets. Output of pagoda.reduce.loading.redundancy
varinfo	Variance information. Output of pagoda.varnorm
env	Gene sets as an environment variable.
pwpca	Weighted PC magnitudes for each gene set provided in the env. Output of pagoda.pathway.wPCA
clpca	Weighted PC magnitudes for de novo gene sets identified by clustering on expression. Output of pagoda.gene.clusters
col.cols	Matrix of column colors. Useful for visualizing cell annotations such as batch labels. Default NULL.
cell.clustering	Dendrogram of cell clustering. Output of pagoda.cluster.cells . Default NULL.
row.clustering	Dendrogram of combined pathways clustering. Default NULL.
title	Title text to be used in the browser label for the app. Default, set as 'pathway clustering'
zlim	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.

Value

PAGODA app

hms-dbmi/scde documentation built on April 19, 2023, 10:21 p.m.