Skip to content

Commit

Permalink
updated
Browse files Browse the repository at this point in the history
  • Loading branch information
poseidonchan committed Oct 11, 2022
1 parent e0392b9 commit 34bae9e
Show file tree
Hide file tree
Showing 25 changed files with 6,874 additions and 5,160 deletions.
38 changes: 35 additions & 3 deletions Experiments/Figures/HIV_analysis.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -168,7 +168,7 @@
" for name in genes:\n",
" if volcano.loc[name]['-Log10 q-value'] > 1.3010:\n",
" overlapping.append(name)\n",
" print(name)\n",
" print(name, volcano.loc[name]['-Log10 q-value'])\n",
" print(len(overlapping))"
]
},
Expand Down Expand Up @@ -223,8 +223,8 @@
"name": "stdout",
"output_type": "stream",
"text": [
"RAB11FIP5\n",
"NOP2\n",
"RAB11FIP5 1.6035579709092302\n",
"NOP2 1.5340047430049137\n",
"2\n"
]
},
Expand Down Expand Up @@ -379,6 +379,16 @@
"id": "f715dac4",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"PTMS 1.6706468765957747\n",
"RAB11FIP5 3.380610720915184\n",
"GALNT10 1.3202918403581017\n",
"3\n"
]
},
{
"data": {
"image/png": "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\n",
Expand All @@ -394,6 +404,7 @@
],
"source": [
"csx_volcano = volcano_data(csx_NK, BNab, Cont)\n",
"detection(csx_volcano)\n",
"volcano_plot(csx_volcano, 1, 1.3010,'CSx_NK')"
]
},
Expand Down Expand Up @@ -442,6 +453,27 @@
"df['Cell Type'] = Cell"
]
},
{
"cell_type": "code",
"execution_count": 19,
"id": "8058068e",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(46, 3)"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df[df['Cell Type'] == 'NK'][df[df['Cell Type'] == 'NK']['Type']=='BNab'].shape"
]
},
{
"cell_type": "code",
"execution_count": 16,
Expand Down
Loading

0 comments on commit 34bae9e

Please sign in to comment.