dot-preprocessData: Preprocess data

Description Usage Arguments Value

Description

Preprocesses input data for .makeServer.

Usage

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.preprocessData(counts, margin, resolutions, assignmentFunction,
  coordinates = NULL)

Arguments

counts

count matrix. rownames should correspond to genes and colnames should correspond to spot coordinates.

margin

which margin of the count matrix to cluster. Valid values are c("spot", "sample", "gene", "feature").

resolutions

vector of resolutions to cluster.

assignmentFunction

function to compute cluster assignments. The function should have the following signature: integer (number of clusters) -> (m, n) feature matrix -> m-length vector (cluster assignment of each data point).

coordinates

optional data.frame with pixel coordinates for each spot. rownames should correspond to the colnames of counts and the columns x and y should specify the pixel coordinates of the spots.

Value

list with the following elements:


jbergenstrahle/SpatialCPie documentation built on April 5, 2020, 7:56 a.m.