pagoda.show.pathways: View pathway or gene weighted PCA

Description Usage Arguments Value

View source: R/functions.R

Description

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

Usage

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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)


scde documentation built on Nov. 8, 2020, 6:19 p.m.