zscoreMatrix: Generate Z-score matrix

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

Generate Z-score matrix

Description

This function provides a heatmap of z-scores resulting from the join count analysis for all possible label pairs.

Usage

zscoreMatrix(sampleInfo, joincount.result)

Arguments

sampleInfo

A data.frame contains the pixel information and cluster labels for each barcode of a human breast cancer 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

joincount.result

calculated result from join count analysis

Value

A data.frame that has a z-score matrix resulting from the join count analysis for all possible label pairs

Examples

fpath <- system.file("extdata", "dataframe.rda", package="stJoincount")
load(fpath)
mosaicIntegration <- rasterizeEachCluster(humanBC)
joincount.result <- joincountAnalysis(mosaicIntegration)
matrix <- zscoreMatrix(humanBC, joincount.result)

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