Interpolate between-spots
Main steps
Step 1：Filter spots that are not in tissue, only reserve the spots with 1 in
in_tissue columnStep 2：Horizontal direction, interpolate new spot between the given spot (x_1, y_1) and its right spot (x_2, y_2)
Step 3：Vertical direction, for one row and its up-adjacent row,
- select two closest spots (x_l, y_l) and (x_r, y_r) in the above row to the given spot (x_o, y_o) in this row,
- interpolate one new spot in two adjacent rows.
[2]:
import os
import numpy as np
import pandas as pd
[3]:
path = '/mnt/lingyu/nfs_share2/Python/'
[4]:
os.chdir(str(path) + 'FineST/FineST/')
import FineST as fst
from FineST.datasets import dataset
import FineST.plottings as fstplt
[5]:
import importlib
import sys
sys.path.append(str(path)+'FineST/FineST/')
import FineST as fst
import FineST.processData
importlib.reload(FineST.processData )
from FineST.processData import *
1. Load and filter original position list
Input: tissue_positions_list.csv file in spatial folder of ST data.
[6]:
patientxy = 'patient1'
os.chdir(str(path)+'FineST/FineST_local/Dataset/NPC/'+str(patientxy)+'/')
position = fst.filter_pos_list('tissue_positions_list.csv')
position
[6]:
| barcode | in_tissue | array_row | array_col | pxl_row_in_fullres | pxl_col_in_fullres | |
|---|---|---|---|---|---|---|
| 33 | GTGTGAGCCGAGGTGC-1 | 1 | 1 | 33 | 1612 | 5423 |
| 35 | GGGAACCACCTGTTTC-1 | 1 | 1 | 35 | 1613 | 5638 |
| 36 | GTTCGTTGCGGACCAG-1 | 1 | 0 | 36 | 1426 | 5745 |
| 37 | TGAGGTTGATCCCAAG-1 | 1 | 1 | 37 | 1613 | 5852 |
| 38 | GATGCCACACTACAGC-1 | 1 | 0 | 38 | 1427 | 5960 |
| ... | ... | ... | ... | ... | ... | ... |
| 3396 | TTCGACAGAGCCCGTG-1 | 1 | 52 | 68 | 11140 | 9153 |
| 3397 | AAGCATACTCTCCTGA-1 | 1 | 53 | 69 | 11327 | 9260 |
| 3398 | GACGACGATCCGCGTT-1 | 1 | 52 | 70 | 11141 | 9368 |
| 3399 | GGTAGAAGACCGCCTG-1 | 1 | 53 | 71 | 11328 | 9474 |
| 3400 | GAGATGGGAGTCGACA-1 | 1 | 52 | 72 | 11141 | 9582 |
1331 rows × 6 columns
2. Interpolate ‘between spots’ in horizontal and vertical directions
[7]:
position_x = fst.inter_spot(position, direction='x')
position_x
[7]:
| array_row | array_col | pxl_row_in_fullres | pxl_col_in_fullres | |
|---|---|---|---|---|
| 0 | 21 | 18 | 5340.5 | 3804.5 |
| 1 | 20 | 19 | 5154.5 | 3912.5 |
| 2 | 22 | 19 | 5527.5 | 3911.5 |
| 3 | 19 | 20 | 4968.0 | 4020.0 |
| 4 | 21 | 20 | 5341.5 | 4019.5 |
| ... | ... | ... | ... | ... |
| 1125 | 38 | 103 | 8537.0 | 12914.0 |
| 1126 | 40 | 103 | 8910.5 | 12913.5 |
| 1127 | 37 | 104 | 8350.5 | 13021.5 |
| 1128 | 39 | 104 | 8724.0 | 13020.5 |
| 1129 | 38 | 105 | 8537.5 | 13128.5 |
1130 rows × 4 columns
[8]:
position_y = fst.inter_spot(position, direction='y')
position_y
[8]:
| array_row | array_col | pxl_row_in_fullres | pxl_col_in_fullres | |
|---|---|---|---|---|
| 0 | 20.5 | 17.5 | 5247.5 | 3751.0 |
| 1 | 21.5 | 17.5 | 5434.0 | 3750.5 |
| 2 | 28.5 | 17.5 | 6740.5 | 3747.0 |
| 3 | 25.5 | 17.5 | 6180.5 | 3748.5 |
| 4 | 19.5 | 18.5 | 5061.0 | 3859.0 |
| ... | ... | ... | ... | ... |
| 2651 | 38.5 | 104.5 | 8630.5 | 13074.5 |
| 2652 | 39.5 | 104.5 | 8817.5 | 13074.0 |
| 2653 | 38.5 | 104.5 | 8631.0 | 13074.5 |
| 2654 | 37.5 | 105.5 | 8444.5 | 13182.5 |
| 2655 | 38.5 | 105.5 | 8631.0 | 13182.0 |
2578 rows × 4 columns
3. Integrate ‘between spot’ and ‘within spot’
position_add: the position list of all between spots (m ~= 3n)
[9]:
position_add = fst.final_pos_list(position_x, position_y, position=None)
position_add
[9]:
| array_row | array_col | pxl_row_in_fullres | pxl_col_in_fullres | |
|---|---|---|---|---|
| 0 | 20.5 | 17.5 | 5247.5 | 3751.0 |
| 1 | 21.5 | 17.5 | 5434.0 | 3750.5 |
| 2 | 25.5 | 17.5 | 6180.5 | 3748.5 |
| 3 | 28.5 | 17.5 | 6740.5 | 3747.0 |
| 4 | 21.0 | 18.0 | 5340.5 | 3804.5 |
| ... | ... | ... | ... | ... |
| 3703 | 38.5 | 104.5 | 8631.0 | 13074.5 |
| 3704 | 39.5 | 104.5 | 8817.5 | 13074.0 |
| 3705 | 38.0 | 105.0 | 8537.5 | 13128.5 |
| 3706 | 37.5 | 105.5 | 8444.5 | 13182.5 |
| 3707 | 38.5 | 105.5 | 8631.0 | 13182.0 |
3708 rows × 4 columns
position_all: the position list of all between spots and all within spot (m+n ~= 4n)
[10]:
position_all = fst.final_pos_list(position_x, position_y, position)
position_all
[10]:
| array_row | array_col | pxl_row_in_fullres | pxl_col_in_fullres | |
|---|---|---|---|---|
| 0 | 50.0 | 0.0 | 10749.0 | 1860.0 |
| 1 | 21.0 | 17.0 | 5341.0 | 3697.0 |
| 2 | 29.0 | 17.0 | 6834.0 | 3693.0 |
| 3 | 20.5 | 17.5 | 5247.5 | 3751.0 |
| 4 | 21.5 | 17.5 | 5434.0 | 3750.5 |
| ... | ... | ... | ... | ... |
| 5034 | 38.0 | 105.0 | 8537.5 | 13128.5 |
| 5035 | 39.0 | 105.0 | 8724.0 | 13128.0 |
| 5036 | 37.5 | 105.5 | 8444.5 | 13182.5 |
| 5037 | 38.5 | 105.5 | 8631.0 | 13182.0 |
| 5038 | 38.0 | 106.0 | 8538.0 | 13236.0 |
5039 rows × 4 columns
[11]:
!pwd
/mnt/lingyu/nfs_share2/Python/FineST/FineST_local/Dataset/NPC/patient1
[ ]:
## save position list to .csv file
position_add.to_csv(str(patientxy)+"_position_add_tissue.csv")
position_all.to_csv(str(patientxy)+"_position_all_tissue.csv")
[13]:
print(position_add.shape[0]/position.shape[0])
print(position_all.shape[0]/position.shape[0])
2.7858752817430505
3.7858752817430505