tp2c.view.pathways {pagoda2}

View pathway or gene-weighted PCA 'Pagoda2' version of the function pagoda.show.pathways() Takes in a list of pathways (or a list of genes), runs weighted PCA, optionally showing the result.

Description

View pathway or gene-weighted PCA 'Pagoda2' version of the function pagoda.show.pathways() Takes in a list of pathways (or a list of genes), runs weighted PCA, optionally showing the result.

Usage

tp2c.view.pathways(
  pathways,
  p2,
  goenv = NULL,
  batch = NULL,
  n.genes = 20,
  two.sided = TRUE,
  n.pc = rep(1, length(pathways)),
  colcols = NULL,
  zlim = NULL,
  labRow = NA,
  vhc = NULL,
  cexCol = 1,
  cexRow = 1,
  nstarts = 50,
  row.order = NULL,
  show.Colv = TRUE,
  plot = TRUE,
  trim = 1.1/nrow(p2$counts),
  showPC = TRUE,
  ...
)

Arguments

pathways

character vector of pathway or gene names

p2

'Pagoda2' object

goenv

environment mapping pathways to genes (default=NULL)

batch

factor (corresponding to rows of the model matrix) specifying batch assignment of each cell, to perform batch correction (default=NULL).

n.genes

integer Number of genes to show (default=20)

two.sided

boolean If TRUE, the set of shown genes should be split among highest and lowest loading (default=TRUE). If FALSE, genes with highest absolute loading should be shown.

n.pc

integer vector Number of principal component to show for each listed pathway(default=rep(1, length(pathways)))

colcols

column color matrix (default=NULL)

zlim

numeric z color limit (default=NULL)

labRow

row labels (default=NA)

vhc

cell clustering (default=NULL)

cexCol

positive numbers, used as cex.axis in for the row or column axis labeling(default=1)

cexRow

positive numbers, used as cex.axis in for the row or column axis labeling(default=1)

nstarts

integer Number of random starts to use (default=50)

row.order

row order (default=NULL). If NULL, uses order from hclust.

show.Colv

boolean Whether to show cell dendrogram (default=TRUE)

plot

boolean Whether to plot (default=TRUE)

trim

numeric Winsorization trim that should be applied (default=1.1/nrow(p2$counts)). Note that p2 is a 'Pagoda2' object.

showPC

boolean (default=TRUE)

...

parameters to pass to my.heatmap2. Only if plot is TRUE.

Value

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