make.pagoda.app: 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