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load10XExpr() Arguments

Argument	Description
visiumDir	A string path to the h5 file with expression information
h5filename	A string of the name of the h5 file in the directory

load10XCoords() Arguments

Argument	Description
visiumDir	A string path to the location of the folder containing the spatial coordinates. The folder in your visiumDir must be named ‘spatial’ and must contain files ‘scalefactors_json.json’ and ‘tissue_positions_list.csv’.
resolution	A string specifying which values to look for in the .json object. Can be either lowres or highres.

Argument	Description
spatialPatterns	A data frame that contains the spatial coordinates for each cell type. The column names must include ‘x’ and ‘y’ as well as a set of numbered columns named ‘Pattern_1…..N’.

Argument	Description
data	A data frame of expression information with rows being the features/genes and columns being the samples/cells.
reconstruction	A data frame of features (rows) and samples (columns) constructed from the information of a latent feature method such as CoGAPs or STdeconvolve. NULL if ‘DE’ mode is specified
optParams	A data frame that for each pattern has the sigmaOpts - the optimal width of the gaussian distribution and the thresOpt - outlier threshold around the set of spots.
spatialPatterns	A data frame that contains the spatial coordinates for each cell type. The column names must include ‘x’ and ‘y’ as well as a set of numbered columns named ‘Pattern_1…..N’.
refPattern	A string of the pattern you want to use to compare to the other patterns in the latent feature space
mode	A string specifying either ‘residual’ mode or ‘DE’ mode for finding interacting genes
minOverlap	a number that specifies the minimum overlap between genes in two patterns to be considered for the statistical tests. The default is 50.
hotspotRegions	a vector that specifies the patterns to compare to the ‘refPattern’. The default is NULL which indicates that all patterns would be compared to the ‘refPattern’.