dataPrepFromSpE: Data Preparation from SpatialExperiment Object

In Nina-Song/stJoincount: stJoincount - Join count statistic for quantifying spatial correlation between clusters

Data Preparation from SpatialExperiment Object

Description

This data preparation function creates a data.frame form Spatial Experiment Object. It extracts the pixel information and cluster labels of each barcode from user's input Seurat Object and generate a data.frame with a certain format which is required for the algorithm. If the user has customized labels, this function will change the column name to "Cluster" when generating the data.frame to make it consist to the required format.

Usage

dataPrepFromSpE(SpeObj, label)

Arguments

SpeObj	input SpatialExperiment object that contains labels for each barcode
label	the column name of the label information in "colData"

Value

A data.frame contains the pixel information and cluster labels for each barcode of the sample. The index contains barcodes, and at least three other columns that have these information are required and the column names should be the same as following: "imagerow": The row pixel coordinate of the center of the spot "imagecol": The column pixel coordinate of the center of the spot "Cluster": The label that corresponding to this barcode

Examples

fpath <- system.file("extdata", "SpeBC.rda", package="stJoincount")
load(fpath)
df <- dataPrepFromSpE(SpeObjBC, "label")

Nina-Song/stJoincount documentation built on Oct. 23, 2022, 4:55 p.m.