Skip to content
This repository has been archived by the owner on Feb 9, 2022. It is now read-only.

Commit

Permalink
Setting up to run pciSeq.
Browse files Browse the repository at this point in the history
  • Loading branch information
@ggirelli
ggirelli committed Sep 14, 2021
1 parent 5be8848 commit f70fef2
Show file tree
Hide file tree
Showing 2 changed files with 252 additions and 0 deletions.
0 notebooks/2_strip.ipynb → notebooks/2.0_strip.ipynb
View file
File renamed without changes.
252 changes: 252 additions & 0 deletions notebooks/2.1_cell_type_calling.ipynb
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,252 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import pandas as pd\n",
"import pciSeq\n",
"import tifffile as tf"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"label_image = tf.imread(\"../data/strip_of_tissue/mask/Base_1_stitched-1.tif.segmented.compressed.tif\")"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"label_image -= 1"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"label_image = label_image.reshape(label_image.shape[-2:])"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(26107, 38994)"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"label_image.shape"
]
},
{
"cell_type": "code",
"execution_count": 40,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/gire/anaconda3/lib/python3.7/site-packages/IPython/core/interactiveshell.py:3063: DtypeWarning: Columns (15) have mixed types.Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
}
],
"source": [
"coords_list = []\n",
"for i in range(28, 35):\n",
" spots_df = pd.read_csv(f\"../data/strip_of_tissue/dw/spots_DW.fov_{i:03d}.csv.gz\", sep=\"\\t\")\n",
" coords_list.append(spots_df.loc[spots_df[\"target\"].values.astype(\"S\") != b'nan', (\"target\", \"xc\", \"yc\")])"
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {},
"outputs": [],
"source": [
"spots_df = pd.concat(coords_list)"
]
},
{
"cell_type": "code",
"execution_count": 39,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>target</th>\n",
" <th>xc</th>\n",
" <th>yc</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>3028</th>\n",
" <td>LHFPL3</td>\n",
" <td>869.844974</td>\n",
" <td>4243.094682</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4913</th>\n",
" <td>CALM2</td>\n",
" <td>909.339057</td>\n",
" <td>4241.631939</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4914</th>\n",
" <td>SLC1A2</td>\n",
" <td>901.862810</td>\n",
" <td>4241.631939</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5076</th>\n",
" <td>FTH1</td>\n",
" <td>822.874646</td>\n",
" <td>4241.469412</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5077</th>\n",
" <td>KCNC2</td>\n",
" <td>808.734789</td>\n",
" <td>4241.469412</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>304824</th>\n",
" <td>SPARCL1</td>\n",
" <td>870.170028</td>\n",
" <td>3912.514586</td>\n",
" </tr>\n",
" <tr>\n",
" <th>304833</th>\n",
" <td>NCAM2</td>\n",
" <td>818.973996</td>\n",
" <td>3912.514586</td>\n",
" </tr>\n",
" <tr>\n",
" <th>304835</th>\n",
" <td>CADM2</td>\n",
" <td>806.459410</td>\n",
" <td>3912.514586</td>\n",
" </tr>\n",
" <tr>\n",
" <th>304836</th>\n",
" <td>FTH1</td>\n",
" <td>804.671612</td>\n",
" <td>3912.514586</td>\n",
" </tr>\n",
" <tr>\n",
" <th>306566</th>\n",
" <td>LHFPL3</td>\n",
" <td>913.402234</td>\n",
" <td>3911.051842</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>47136 rows × 3 columns</p>\n",
"</div>"
],
"text/plain": [
" target xc yc\n",
"3028 LHFPL3 869.844974 4243.094682\n",
"4913 CALM2 909.339057 4241.631939\n",
"4914 SLC1A2 901.862810 4241.631939\n",
"5076 FTH1 822.874646 4241.469412\n",
"5077 KCNC2 808.734789 4241.469412\n",
"... ... ... ...\n",
"304824 SPARCL1 870.170028 3912.514586\n",
"304833 NCAM2 818.973996 3912.514586\n",
"304835 CADM2 806.459410 3912.514586\n",
"304836 FTH1 804.671612 3912.514586\n",
"306566 LHFPL3 913.402234 3911.051842\n",
"\n",
"[47136 rows x 3 columns]"
]
},
"execution_count": 39,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"res = pciSeq.fit(spots_df, label_image, scRNA_df)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"res = pciSeq.fit(spots_df, label_image, scRNA_df)"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
}
},
"nbformat": 4,
"nbformat_minor": 4
}

0 comments on commit f70fef2

Please sign in to comment.