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