p2.make.pagoda1.app {pagoda2}

Create 'PAGODA1' web application from a 'Pagoda2' object 'PAGODA1' found here, with 'SCDE': <https://www.bioconductor.org/packages/release/bioc/html/scde.html>

Description

Create 'PAGODA1' web application from a 'Pagoda2' object 'PAGODA1' found here, with 'SCDE': <https://www.bioconductor.org/packages/release/bioc/html/scde.html>

Usage

p2.make.pagoda1.app(
  p2,
  col.cols = NULL,
  row.clustering = NULL,
  title = "pathway clustering",
  zlim = NULL,
  embedding = NULL,
  inner.clustering = TRUE,
  groups = NULL,
  clusterType = NULL,
  embeddingType = NULL,
  veloinfo = NULL,
  type = "PCA",
  min.group.size = 1,
  batch.colors = NULL,
  n.cores = 10
)

Arguments

p2

'Pagoda2' object

col.cols

Matrix of column colors (default=NULL). Useful for visualizing cell annotations such as batch labels.

row.clustering

Row dendrogram (default=NULL)

title

character Title to use (default="pathway clustering")

zlim

Range of the normalized gene expression levels (default=NULL). Input as a list: c(lower_bound, upper_bound). Values outside this range will be Winsorized. Useful for increasing the contrast of the heatmap visualizations. If NULL, set to the 5th and 95th percentiles.

embedding

A 2-D embedding of the cells (PCA, tSNE, etc.), passed as a data frame with two columns (two dimensions) and rows corresponding to cells (row names have to match cell names) (default=NULL).

inner.clustering

boolean Whether to get overall cell clustering (default=TRUE).

groups

factor describing grouping of different cells. If provided, the cross-fits and the expected expression magnitudes will be determined separately within each group. The factor should have the same length as ncol(counts) (default=NULL).

clusterType

cluster type (default=NULL). If NULL, takes the latest cluster in the 'Pagoda2' object using 'p2$clusters[[type]][[1]]'

embeddingType

embedding type (default=NULL). If NULL, takes the latest embedding in the 'Pagoda2' object using p2$embeddings[[type]][[1]]

veloinfo

cell velocity information, cell velocities (grid and cell) (default=NULL)

type

character Either 'counts' or a name of a 'reduction' in the 'Pagoda2' object (default='PCA')

min.group.size

integer Minimum group size (default=1)

batch.colors

colors of the batches, i.e. the factor (corresponding to rows of the model matrix) specifying batch assignment of each cell(default=NULL)

n.cores

numeric Number of cores (default=10)

Value

'PAGODA1' web application