sccross.utils

Miscellaneous utilities

Functions

all_counts	Check whether an array contains all counts
col_pcc	Column-wise Pearson’s correlation coefficient (sparse friendly)
col_spr	Column-wise Spearman’s rank correlation
col_var	Column-wise variance (sparse friendly)
cov_mat	Covariance matrix (sparse friendly)
densify	Convert a matrix to dense regardless of original type.
get_chained_attr	Get attribute from an object, with support for chained attribute names.
get_rs	Get random state object
in_ipynb	Determine whether running in an ipynb environment.
logged	Add logger as an attribute
pcc_mat	Pearson’s correlation coefficient (sparse friendly)
prob_or	Combined multiple probabilities in a logical OR manner.
prod	Product of elements
run_command	Run an external command and get realtime output
sigmoid	The sigmoid function in numpy
smart_tqdm	Use tqdm.tqdm or tqdm.tqdm_notebook adaptively based on return value of in_ipynb().
spr_mat	Spearman’s rank correlation
tfidf	TF-IDF normalization (following the Seurat v3 approach)

Classes

ConfigManager	Global configurations
ConstrainedDataFrame	Data frame with certain format constraints
DelayedKeyboardInterrupt	Shield a code block from keyboard interruptions, delaying handling till the block is finished (adapted from https://stackoverflow.com/a/21919644).
LogManager	Manage loggers used in the package
SingletonMeta	Ensure singletons via a meta class