Table 2.

Description of FLocK features. If the pre-defined cluster type number is set to zero, we have feature set A, these are the features that do not consider a pre-defined cluster types. If the predefined cluster number is set to >1, we have feature set B, these are the features that do consider a pre-defined cluster types. For more details on these feature names and the corresponding computation, we direct the reader to appendix 1 and to the code released on Github (Lu, 2020).

A. Features that do not consider cluster types
Feature groups	#	Feature names	Explanation
Intersection between different FLocKs	44	Portion/ number of intersected FLocKs, mean intersected area	Quantify the interaction between FLocKs
Size of FLocK	12	Size of FLocK, nuclei number in FLocK	Quantify the size of FLocKs
Disorder of nuclear morphology	18	Variation in nuclear morphology within a FLocK	Quantify disorder of nuclear morphology locally
Spatial arrangement of FLocKs	102	Global graph measurements	Quantify global architecture of FLocKs
B. Features that consider cluster types (k is the number of cluster types).
Feature groups	#	Feature names	Explanation
Intersection between different types of FLocKs	2xk	Portion of intersected FLocKs from different cluster types	Portion of intersected FLocKs, quantifying the intersection between different types (intertype) and within same type (intra-type) of FLocKs
Enrichment of the K-nearest FLocKs	24	Portion of other types of FLocKs within 5, 10, 15 nearest neighbors	Quantify the diversity of FLocKs, with pre-defined phenotype number, in terms of nearest neighbors
Spatial arrangement of a specific type of FLocK	44xk	Global graph measurements based on a specific type of FLocK	Quantify the diversity of a specific type of FLocK, in terms of nearest neighbors