pagoda.show.pathways {scde} | R Documentation

## View pathway or gene weighted PCA

### Description

Takes in a list of pathways (or a list of genes), runs weighted PCA, optionally showing the result.

### Usage

    pagoda.show.pathways(pathways, varinfo, goenv = NULL, n.genes = 20,
      two.sided = FALSE, n.pc = rep(1, length(pathways)), colcols = NULL,
      zlim = NULL, showRowLabels = FALSE, cexCol = 1, cexRow = 1,
      nstarts = 10, cell.clustering = NULL, show.cell.dendrogram = TRUE,
      plot = TRUE, box = TRUE, trim = 0, return.details = FALSE, ...)

### Arguments

`pathways` | character vector of pathway or gene names
`varinfo` | output of pagoda.varnorm()
`goenv` | environment mapping pathways to genes
`n.genes` | number of genes to show
`two.sided` | whether the set of shown genes should be split among highest and lowest loading (T) or if genes with highest absolute loading (F) should be shown
`n.pc` | optional integer vector giving the number of principal component to show for each listed pathway
`colcols` | optional column color matrix
`zlim` | optional z color limit
`showRowLabels` | controls whether row labels are shown in the plot
`cexCol` | column label size (cex)
`cexRow` | row label size (cex)
`nstarts` | number of random starts for the wPCA
`cell.clustering` | cell clustering
`show.cell.dendrogram` | whether cell dendrogram should be shown
`plot` | whether the plot should be shown
`box` | whether to draw a box around the plotted matrix
`trim` | optional Winsorization trim that should be applied
`return.details` | whether the function should return the matrix as well as full PCA info instead of just PC1 vector
`...` | additional arguments are passed to the `c.view.pathways`

### Value

cell scores along the first principal component of shown genes (returned as invisible)

[Package scde version 2.12.0 Index]