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@poseidonchan
poseidonchan committed Sep 24, 2022
1 parent 3768956 commit e0392b9
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Showing 3 changed files with 107 additions and 95 deletions.
159 changes: 91 additions & 68 deletions Experiments/Figures/concordance_analysis.ipynb
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},
{
"cell_type": "code",
"execution_count": 31,
"execution_count": 4,
"id": "4f15725c",
"metadata": {},
"outputs": [],
"source": [
"data8k = pd.read_csv('~/Downloads/data8k_ref.txt',sep='\\t',index_col=0)\n",
"monaco = pd.read_csv('~/Downloads/monaco_groupmode1/monaco_group_GEP.txt',sep='\\t',index_col=0)"
"monaco = pd.read_csv(\"/Users/chan/Desktop/Chan's Research/2021Summer Intern/MajorReview/GEPbenchmarking/monaco_groupmode/monaco_group_GEP.txt\",sep='\\t',index_col=0)"
]
},
{
"cell_type": "code",
"execution_count": 55,
"id": "5f70e38f",
"metadata": {},
"outputs": [],
"source": [
"monaco = pd.read_csv('~/Downloads/monaco_pbmc.txt',sep='\\t',index_col=0)"
]
},
{
"cell_type": "code",
"execution_count": 58,
"id": "0b759f0e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"0.9719791845370847\n",
"0.9552810659346943\n",
"0.9695774003545491\n",
"0.9655744267169898\n",
"0.9681477669125637\n",
"0.9707782924458169\n",
"0.9809572825527535\n",
"0.9774689769543089\n",
"0.9755246754732086\n",
"0.9767255675644765\n",
"0.972836964602276\n",
"0.9703779950820609\n"
]
}
],
"source": [
"for i in range(monaco.shape[1]):\n",
" print(np.sum(monaco.iloc[:,i]>0)/17487)"
]
},
{
"cell_type": "markdown",
"id": "93d9e16e",
"metadata": {},
"source": []
},
{
"cell_type": "code",
"execution_count": 32,
"execution_count": 5,
"id": "fe5dbc42",
"metadata": {},
"outputs": [],
Expand All @@ -102,7 +56,7 @@
},
{
"cell_type": "code",
"execution_count": 33,
"execution_count": 6,
"id": "eb8c1f4a",
"metadata": {},
"outputs": [],
Expand All @@ -113,7 +67,7 @@
},
{
"cell_type": "code",
"execution_count": 34,
"execution_count": 7,
"id": "b03ae3d0",
"metadata": {},
"outputs": [],
Expand All @@ -123,7 +77,7 @@
},
{
"cell_type": "code",
"execution_count": 35,
"execution_count": 8,
"id": "feff6471",
"metadata": {},
"outputs": [],
Expand All @@ -134,7 +88,7 @@
},
{
"cell_type": "code",
"execution_count": 36,
"execution_count": 9,
"id": "28a03c4a",
"metadata": {},
"outputs": [],
Expand All @@ -145,7 +99,7 @@
},
{
"cell_type": "code",
"execution_count": 37,
"execution_count": 10,
"id": "7cd3bd8e",
"metadata": {},
"outputs": [],
Expand All @@ -158,7 +112,7 @@
},
{
"cell_type": "code",
"execution_count": 38,
"execution_count": 11,
"id": "0dc8eaea",
"metadata": {},
"outputs": [],
Expand All @@ -169,7 +123,7 @@
},
{
"cell_type": "code",
"execution_count": 39,
"execution_count": 12,
"id": "a336c079",
"metadata": {},
"outputs": [
Expand All @@ -193,7 +147,7 @@
},
{
"cell_type": "code",
"execution_count": 40,
"execution_count": 13,
"id": "a2470b53",
"metadata": {},
"outputs": [],
Expand All @@ -208,18 +162,43 @@
},
{
"cell_type": "code",
"execution_count": 54,
"execution_count": 19,
"id": "c5bcdc41",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.06275639548765453"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"real_gene_ccc = np.array(real_gene_ccc)\n",
"np.median(real_gene_ccc[~np.isnan(real_gene_ccc)])"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "0ee93808",
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"The PostScript backend does not support transparency; partially transparent artists will be rendered opaque.\n"
]
"data": {
"text/plain": [
"Text(0.02, 0.5, 'adapt2real')"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
},
{
"data": {
Expand Down Expand Up @@ -291,7 +270,7 @@
},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 20,
"id": "ef8e4960",
"metadata": {},
"outputs": [],
Expand All @@ -303,7 +282,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 21,
"id": "b175c6e5",
"metadata": {},
"outputs": [
Expand All @@ -328,7 +307,7 @@
},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": 22,
"id": "737b925d",
"metadata": {},
"outputs": [],
Expand All @@ -341,6 +320,28 @@
" real_gene_ccc.append(CCCscore(testsigm[:,i],orisigm[:,i]))"
]
},
{
"cell_type": "code",
"execution_count": 23,
"id": "b7127d8a",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.21708191995376117"
]
},
"execution_count": 23,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"real_gene_ccc = np.array(real_gene_ccc)\n",
"np.median(real_gene_ccc[~np.isnan(real_gene_ccc)])"
]
},
{
"cell_type": "code",
"execution_count": 4,
Expand Down Expand Up @@ -382,7 +383,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 24,
"id": "d8d1012a",
"metadata": {},
"outputs": [
Expand All @@ -407,7 +408,7 @@
},
{
"cell_type": "code",
"execution_count": 31,
"execution_count": 25,
"id": "cdd1a040",
"metadata": {},
"outputs": [],
Expand All @@ -420,6 +421,28 @@
" simu_gene_ccc.append(CCCscore(trainsigm[:,i],orisigm[:,i]))"
]
},
{
"cell_type": "code",
"execution_count": 26,
"id": "3e19fcf0",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.22809295097698173"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"simu_gene_ccc = np.array(simu_gene_ccc)\n",
"np.median(simu_gene_ccc[~np.isnan(simu_gene_ccc)])"
]
},
{
"cell_type": "code",
"execution_count": 5,
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39 changes: 15 additions & 24 deletions Experiments/Figures/heat_map/heat map.ipynb
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4 changes: 1 addition & 3 deletions README.md
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related article ***Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis*** is available on [*bioRxiv*](https://doi.org/10.1101/2021.10.26.465846)

## Warning
The data I uploaded to the tsinghua cloud has been removed since I left Tsinghua University😭. If you need these files, please contact me (poseidonchan@icloud.com).

Currently, I am busy with moving to a new places. The version 1.0.3 is still not tested yet. If you want to reproduce the results in the manuscript, please find the notebooks in the Experiments folder and contact me (poseidonchan@icloud.com).
The data I uploaded to the tsinghua cloud has been removed since I left Tsinghua University. If you need these files, please contact me (poseidonchan@icloud.com).

## Setup

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