pagoda.view.aspects {scde} | R Documentation

## 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)

[Package scde version 2.20.0 Index]