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

stJoincount, the application of join count analysis to the spatial transcriptomics dataset. This tool converts the spatial map into a raster object (a two-dimensional image as a rectangular matrix or grid of square pixels), where clusters labelled spots are converted to adjacent pixels with a calculated resolution. A neighbors' list was created based on the rasterized sample, which identifies adjacent and diagonal neighbors for each pixel. After adding binary spatial weights to the neighbors' list, a multi-categorical join count analysis is then performed, allowing all possible combinations of cluster pairings to be tabulated. The function returns the observed join counts, the expected count under conditions of spatial randomness, and the variance of observed to expected calculated under non-free sampling. The z-score is then calculated as the difference between observed and expected counts, divided by the square root of the variance.

install.packages("remotes")
remotes::install_github("Nina-Song/stJoincount")