pagoda.view.aspects: View PAGODA output

In hms-dbmi/scde: Single Cell Differential Expression

View PAGODA output

Description

Create static image of PAGODA output visualizing cell hierarchy and top aspects of transcriptional heterogeneity

Usage

pagoda.view.aspects(tamr, row.clustering = hclust(dist(tamr$xv)), top = Inf,
  ...)

Arguments

tamr	Combined pathways that show similar expression patterns. Output of pagoda.reduce.redundancy
row.clustering	Dendrogram of combined pathways clustering
top	Restrict output to the top n aspects of heterogeneity
...	additional arguments are passed to the view.aspects method during plotting

Value

PAGODA heatmap

Examples

data(pollen)
cd <- clean.counts(pollen)

knn <- knn.error.models(cd, k=ncol(cd)/4, n.cores=10, min.count.threshold=2, min.nonfailed=5, max.model.plots=10)
varinfo <- pagoda.varnorm(knn, counts = cd, trim = 3/ncol(cd), max.adj.var = 5, n.cores = 1, plot = FALSE)
pwpca <- pagoda.pathway.wPCA(varinfo, go.env, n.components=1, n.cores=10, n.internal.shuffles=50)
tam <- pagoda.top.aspects(pwpca, return.table = TRUE, plot=FALSE, z.score=1.96)  # top aspects based on GO only
pagoda.view.aspects(tam)

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