.. _`gene_profiling`:
========================================
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]
  
.. image:: ../_static/gene_profiling_workflow.png
    :alt: Title figure
    :width: 700px
    :align: center


**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)
================================= ===========================================================