tp2c.view.pathways: View pathway or gene-weighted PCA 'Pagoda2' version of the...

In pagoda2: Single Cell Analysis and Differential Expression

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)

pagoda2 documentation built on June 24, 2024, 9:09 a.m.