| 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’. |