Gradient Gene Profiling¶
The basic idea here is converting 3D data into 1D pseudoBulk data.To achieve this, we choose a body axis ( an idx of spatial coordinate ) and group data into equal-width bins.Cells of each bin then merge into one meta cell.
Usage¶
usage: AP_Profiling [-h] -i INPUT -o OUTPUT [-m MIN_BIN] [-n NUM_HVG] [-b BIN_NUM]
Create AP Profiling for genes.
argument |
description |
|---|---|
-h, –help |
show this help message and exit |
-i INPUT, –input INPUT |
the input adata, Notice: we expect raw count matrix!!! |
-o OUTPUT, –output OUTPUT |
the output prefix |
-m MIN_BIN, –min_bin MIN_BIN |
the minimum allowed cell number of a bin, default(50) |
-n NUM_HVG, –num_HVG NUM_HVG |
the number of HVG bin, default(5000) |
-b BIN_NUM, –bin_num BIN_NUM |
the total bin number, default(100) |