make.pagoda.app {scde} | R Documentation

## 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

[Package scde version 2.12.0 Index]