From b8f20bf7d4272e3693f4f79a02a915d39eb05041 Mon Sep 17 00:00:00 2001 From: ASPP Student Date: Wed, 28 Aug 2024 12:59:24 +0300 Subject: [PATCH] descriptive stats --- exercises/pandas_intro/pandas_intro.ipynb | 1249 ++++++++++++++++++++- 1 file changed, 1218 insertions(+), 31 deletions(-) diff --git a/exercises/pandas_intro/pandas_intro.ipynb b/exercises/pandas_intro/pandas_intro.ipynb index 0ecc796..5d7e490 100644 --- a/exercises/pandas_intro/pandas_intro.ipynb +++ b/exercises/pandas_intro/pandas_intro.ipynb @@ -10,7 +10,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 4, "id": "f7777604", "metadata": {}, "outputs": [], @@ -32,12 +32,12 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 31, "id": "9ca3bec6", "metadata": {}, "outputs": [], "source": [ - "df = pd.read_csv('../../data/QC_passed_2024-07-04_collected.csv')" + "df = pd.read_csv('./QC_passed_2024-07-04_collected.csv')" ] }, { @@ -50,11 +50,24 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "id": "4b68e5a6", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/plain": [ + "(827, 31)" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.shape" + ] }, { "cell_type": "markdown", @@ -66,11 +79,291 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "id": "4adcd5bf", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/html": [ + "
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OPfilenameslicecell_chcell_IDdaytreatmenthrs_incubationrepatchhrs_after_OPRsRinresting_potentialmax_spikesRheobaseAP_heigthTHmax_depolmax_repolmembra_time_constant_taucapacitancecommentsrheo_rampAP_halfwidthRheobse_rampUnnamed: 27rheos_rampcommenthigh K concentrationRMP_from_char
0OP23042023420003.abfS1123420S1c1D1TTX0.0no10.4163896.67564339.025301-74.28588924200.080.749512-35.278320336.181641-60.79101619.40510.6017670753.3801131.151009NaNNaNNaNNaNNaN8 mM-61.828554
1OP23042023420003.abfS1323420S1c3D1TTX0.0no10.4163897.86717448.728367-69.57397526300.078.448486-32.043457350.097656-67.13867217.30393.3979181585.1028371.006321NaNNaNNaNNaNNaN8 mM-60.460298
2OP23042023420003.abfS1623420S1c6D1TTX0.0no10.4163898.82013435.971082-54.95605522300.076.660156-29.827881270.629883-52.24609414.85426.0987743173.9157971.266335NaNNaNNaNNaNNaN8 mM-59.615979
3OP23042023420003.abfS1723420S1c7D1TTX0.0yes10.4163897.26919539.186101-69.26879924300.075.030518-29.699707242.553711-71.41113317.15478.2733624598.0799360.994396NaNNaNNaNNaNNaN8 mM-61.173839
4OP23042023420003.abfS1823420S1c8D1TTX0.0yes10.4163896.00040031.599917-70.55053722350.081.011963-33.068848309.448242-61.40136716.65575.5139245786.9278981.182830NaNNaNNaNNaNNaN8 mM-60.956350
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" + ], + "text/plain": [ + " OP filename slice cell_ch cell_ID day treatment \\\n", + "0 OP230420 23420003.abf S1 1 23420S1c1 D1 TTX \n", + "1 OP230420 23420003.abf S1 3 23420S1c3 D1 TTX \n", + "2 OP230420 23420003.abf S1 6 23420S1c6 D1 TTX \n", + "3 OP230420 23420003.abf S1 7 23420S1c7 D1 TTX \n", + "4 OP230420 23420003.abf S1 8 23420S1c8 D1 TTX \n", + "\n", + " hrs_incubation repatch hrs_after_OP Rs Rin \\\n", + "0 0.0 no 10.416389 6.675643 39.025301 \n", + "1 0.0 no 10.416389 7.867174 48.728367 \n", + "2 0.0 no 10.416389 8.820134 35.971082 \n", + "3 0.0 yes 10.416389 7.269195 39.186101 \n", + "4 0.0 yes 10.416389 6.000400 31.599917 \n", + "\n", + " resting_potential max_spikes Rheobase AP_heigth TH max_depol \\\n", + "0 -74.285889 24 200.0 80.749512 -35.278320 336.181641 \n", + "1 -69.573975 26 300.0 78.448486 -32.043457 350.097656 \n", + "2 -54.956055 22 300.0 76.660156 -29.827881 270.629883 \n", + "3 -69.268799 24 300.0 75.030518 -29.699707 242.553711 \n", + "4 -70.550537 22 350.0 81.011963 -33.068848 309.448242 \n", + "\n", + " max_repol membra_time_constant_tau capacitance comments rheo_ramp \\\n", + "0 -60.791016 19.40 510.601767 0 753.380113 \n", + "1 -67.138672 17.30 393.397918 1 585.102837 \n", + "2 -52.246094 14.85 426.098774 3 173.915797 \n", + "3 -71.411133 17.15 478.273362 4 598.079936 \n", + "4 -61.401367 16.65 575.513924 5 786.927898 \n", + "\n", + " AP_halfwidth Rheobse_ramp Unnamed: 27 rheos_ramp comment \\\n", + "0 1.151009 NaN NaN NaN NaN NaN \n", + "1 1.006321 NaN NaN NaN NaN NaN \n", + "2 1.266335 NaN NaN NaN NaN NaN \n", + "3 0.994396 NaN NaN NaN NaN NaN \n", + "4 1.182830 NaN NaN NaN NaN NaN \n", + "\n", + " high K concentration RMP_from_char \n", + "0 8 mM -61.828554 \n", + "1 8 mM -60.460298 \n", + "2 8 mM -59.615979 \n", + "3 8 mM -61.173839 \n", + "4 8 mM -60.956350 " + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.head(5)" + ] }, { "cell_type": "markdown", @@ -82,11 +375,55 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 15, "id": "64df567c", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/plain": [ + "OP object\n", + "filename object\n", + "slice object\n", + "cell_ch int64\n", + "cell_ID object\n", + "day object\n", + "treatment object\n", + "hrs_incubation float64\n", + "repatch object\n", + "hrs_after_OP float64\n", + "Rs float64\n", + "Rin float64\n", + "resting_potential float64\n", + "max_spikes int64\n", + "Rheobase float64\n", + "AP_heigth float64\n", + "TH float64\n", + "max_depol float64\n", + "max_repol float64\n", + "membra_time_constant_tau float64\n", + "capacitance float64\n", + "comments object\n", + "rheo_ramp float64\n", + "AP_halfwidth float64\n", + "Rheobse_ramp float64\n", + "Unnamed: 27 float64\n", + "rheos_ramp float64\n", + "comment object\n", + " float64\n", + "high K concentration object\n", + "RMP_from_char float64\n", + "dtype: object" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.dtypes" + ] }, { "cell_type": "markdown", @@ -98,11 +435,25 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "id": "b90ce541", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/plain": [ + "array(['TTX', 'high K', 'Ctrl', 'wash in high K'], dtype=object)" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df[\"high K concentration\"].unique()\n", + "df[\"treatment\"].unique()" + ] }, { "cell_type": "markdown", @@ -114,11 +465,32 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "id": "e2b86159", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/plain": [ + "count 827.000000\n", + "mean 27.920193\n", + "std 57.997378\n", + "min 0.000000\n", + "25% 19.000000\n", + "50% 26.000000\n", + "75% 33.000000\n", + "max 1664.000000\n", + "Name: max_spikes, dtype: float64" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df[\"max_spikes\"].describe()" + ] }, { "cell_type": "markdown", @@ -130,11 +502,492 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 19, "id": "c449e9ff", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/html": [ + "
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OPfilenameslicecell_chcell_IDdaytreatmenthrs_incubationrepatchhrs_after_OPRsRinresting_potentialmax_spikesRheobaseAP_heigthTHmax_depolmax_repolmembra_time_constant_taucapacitancecommentsrheo_rampAP_halfwidthRheobse_rampUnnamed: 27rheos_rampcommenthigh K concentrationRMP_from_char
70OP23113023n30003.abfS1123n30S1c1D1Ctrl0.0yes11.99277815.62708158.666581-78.06091355300.088.775635-41.577148352.294922-103.51562513.80329.3506190NaN0.811086351.581719NaNNaNNaNNaN8 mM-71.584465
74OP23113023n30037.abfS1_D2223n30S1_D2c2D2wash in high K21.0no32.6994447.42644265.804793-67.54455661250.077.716064-36.505127246.459961-74.34082012.50200.2933988; exclude; Rs_end > 30NaN0.950158322.090736NaNNaNNaNNaN8 mM-59.579331
262OP23080823808003.abfS1623808S1c6D1TTX0.0no8.16333310.394754106.082649-83.3007811664-300.071.081543-15.057373237.426758-69.70214813.0598.9408615NaN1.025354NaNNaNNaNNaNNaN8 mM-32.684415
321OP23020923209012.abfS2523209S2c5D1high K0.0no-2.8747228.52573081.231493-69.04907253100.082.275391-34.912109365.478516-98.26660213.05141.8316428192.0246010.713136NaNNaNNaNNaNNaN8 mM-58.246034
396OP23081023810004.abfS1523810S1c5D1high K0.0yes5.66083325.46841279.043216-65.15502955100.085.491943-43.072510389.770508-80.07812511.45241.5927883224.5875000.966593NaNNaNNaNNaNNaN8 mM-60.860893
397OP23081023810004.abfS1723810S1c7D1high K0.0yes5.66083326.75653074.709503-64.85595753150.090.942383-42.932129423.950195-83.0078129.10239.3168545307.5403000.965371NaNNaNNaNNaNNaN8 mM-61.513494
398OP23081023810004.abfS1823810S1c8D1high K0.0no5.66083318.02366563.532613-61.41357455200.084.509277-39.605713339.843750-77.3925787.10146.6915516199.5067001.043352NaNNaNNaNNaNNaN8 mM-62.291177
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647OP24011724118004.abfS2_D2524117S2_D2c5D1Ctrl20.0no26.42420027.929918140.091217-70.42236356100.082.684326-44.421387325.561523-96.92382818.85226.1723914NaN0.769121207.006900NaNNaNNaNNaN8 mM-60.495223
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" + ], + "text/plain": [ + " OP filename slice cell_ch cell_ID day treatment \\\n", + "70 OP231130 23n30003.abf S1 1 23n30S1c1 D1 Ctrl \n", + "74 OP231130 23n30037.abf S1_D2 2 23n30S1_D2c2 D2 wash in high K \n", + "262 OP230808 23808003.abf S1 6 23808S1c6 D1 TTX \n", + "321 OP230209 23209012.abf S2 5 23209S2c5 D1 high K \n", + "396 OP230810 23810004.abf S1 5 23810S1c5 D1 high K \n", + "397 OP230810 23810004.abf S1 7 23810S1c7 D1 high K \n", + "398 OP230810 23810004.abf S1 8 23810S1c8 D1 high K \n", + "558 OP230314 23314003.abf S1 8 23314S1c8 D1 high K \n", + "646 OP240117 24118004.abf S2_D2 4 24117S2_D2c4 D1 Ctrl \n", + "647 OP240117 24118004.abf S2_D2 5 24117S2_D2c5 D1 Ctrl \n", + "\n", + " hrs_incubation repatch hrs_after_OP Rs Rin \\\n", + "70 0.0 yes 11.992778 15.627081 58.666581 \n", + "74 21.0 no 32.699444 7.426442 65.804793 \n", + "262 0.0 no 8.163333 10.394754 106.082649 \n", + "321 0.0 no -2.874722 8.525730 81.231493 \n", + "396 0.0 yes 5.660833 25.468412 79.043216 \n", + "397 0.0 yes 5.660833 26.756530 74.709503 \n", + "398 0.0 no 5.660833 18.023665 63.532613 \n", + "558 0.0 no 5.940833 22.054204 97.596130 \n", + "646 20.0 no 26.424200 17.188385 139.095453 \n", + "647 20.0 no 26.424200 27.929918 140.091217 \n", + "\n", + " resting_potential max_spikes Rheobase AP_heigth TH \\\n", + "70 -78.060913 55 300.0 88.775635 -41.577148 \n", + "74 -67.544556 61 250.0 77.716064 -36.505127 \n", + "262 -83.300781 1664 -300.0 71.081543 -15.057373 \n", + "321 -69.049072 53 100.0 82.275391 -34.912109 \n", + "396 -65.155029 55 100.0 85.491943 -43.072510 \n", + "397 -64.855957 53 150.0 90.942383 -42.932129 \n", + "398 -61.413574 55 200.0 84.509277 -39.605713 \n", + "558 -67.358398 52 100.0 79.431152 -41.333008 \n", + "646 -76.916504 61 100.0 78.436279 -40.686035 \n", + "647 -70.422363 56 100.0 82.684326 -44.421387 \n", + "\n", + " max_depol max_repol membra_time_constant_tau capacitance \\\n", + "70 352.294922 -103.515625 13.80 329.350619 \n", + "74 246.459961 -74.340820 12.50 200.293398 \n", + "262 237.426758 -69.702148 13.05 98.940861 \n", + "321 365.478516 -98.266602 13.05 141.831642 \n", + "396 389.770508 -80.078125 11.45 241.592788 \n", + "397 423.950195 -83.007812 9.10 239.316854 \n", + "398 339.843750 -77.392578 7.10 146.691551 \n", + "558 325.073242 -111.572266 13.30 186.404790 \n", + "646 316.040039 -95.092773 19.80 201.367598 \n", + "647 325.561523 -96.923828 18.85 226.172391 \n", + "\n", + " comments rheo_ramp AP_halfwidth Rheobse_ramp \\\n", + "70 0 NaN 0.811086 351.581719 \n", + "74 8; exclude; Rs_end > 30 NaN 0.950158 322.090736 \n", + "262 5 NaN 1.025354 NaN \n", + "321 8 192.024601 0.713136 NaN \n", + "396 3 224.587500 0.966593 NaN \n", + "397 5 307.540300 0.965371 NaN \n", + "398 6 199.506700 1.043352 NaN \n", + "558 5 NaN 0.776089 NaN \n", + "646 3 NaN 0.740537 295.539851 \n", + "647 4 NaN 0.769121 207.006900 \n", + "\n", + " Unnamed: 27 rheos_ramp comment high K concentration RMP_from_char \n", + "70 NaN NaN NaN NaN 8 mM -71.584465 \n", + "74 NaN NaN NaN NaN 8 mM -59.579331 \n", + "262 NaN NaN NaN NaN 8 mM -32.684415 \n", + "321 NaN NaN NaN NaN 8 mM -58.246034 \n", + "396 NaN NaN NaN NaN 8 mM -60.860893 \n", + "397 NaN NaN NaN NaN 8 mM -61.513494 \n", + "398 NaN NaN NaN NaN 8 mM -62.291177 \n", + "558 NaN 201.505075 NaN NaN 8 mM -61.035575 \n", + "646 NaN NaN NaN NaN 8 mM -59.561161 \n", + "647 NaN NaN NaN NaN 8 mM -60.495223 " + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "spikes_larger_50 =(df[\"max_spikes\"] > 50)\n", + "df[spikes_larger_50]" + ] }, { "cell_type": "markdown", @@ -148,11 +1001,35 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 22, "id": "8b84faa2", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/plain": [ + "count 353.000000\n", + "mean 23.844193\n", + "std 10.519791\n", + "min 0.000000\n", + "25% 18.000000\n", + "50% 24.000000\n", + "75% 31.000000\n", + "max 48.000000\n", + "Name: max_spikes, dtype: float64" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "k_c_8 = (df[\"high K concentration\"] == '8 mM')\n", + "k_c_15 = (df[\"high K concentration\"] == '15 mM')\n", + "df[k_c_8][\"max_spikes\"].describe()\n", + "df[k_c_15][\"max_spikes\"].describe()\n" + ] }, { "cell_type": "markdown", @@ -166,11 +1043,33 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 23, "id": "1201f7d1", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/plain": [ + "count 473.000000\n", + "mean 27.503171\n", + "std 10.965493\n", + "min 1.000000\n", + "25% 21.000000\n", + "50% 27.000000\n", + "75% 34.000000\n", + "max 61.000000\n", + "Name: max_spikes, dtype: float64" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "KM = k_c_8 & (df[\"max_spikes\"]<= 100)\n", + "df[KM][\"max_spikes\"].describe()" + ] }, { "cell_type": "markdown", @@ -188,11 +1087,299 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 32, "id": "1cf5c15d", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/html": [ + "
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OPfilenameslicecell_chcell_IDdaytreatmenthrs_incubationrepatchhrs_after_OPRsRinresting_potentialmax_spikesRheobaseAP_heigthTHmax_depolmax_repolmembra_time_constant_taucapacitancecommentsrheo_rampAP_halfwidthRheobse_rampUnnamed: 27rheos_rampcommenthigh K concentrationRMP_from_charK (mM)
0OP23042023420003.abfS1123420S1c1D1TTX0.0no10.4163896.67564339.025301-74.28588924200.080.749512-35.278320336.181641-60.79101619.40510.6017670753.3801131.151009NaNNaNNaNNaNNaN8 mM-61.8285548.0
1OP23042023420003.abfS1323420S1c3D1TTX0.0no10.4163897.86717448.728367-69.57397526300.078.448486-32.043457350.097656-67.13867217.30393.3979181585.1028371.006321NaNNaNNaNNaNNaN8 mM-60.4602988.0
2OP23042023420003.abfS1623420S1c6D1TTX0.0no10.4163898.82013435.971082-54.95605522300.076.660156-29.827881270.629883-52.24609414.85426.0987743173.9157971.266335NaNNaNNaNNaNNaN8 mM-59.6159798.0
3OP23042023420003.abfS1723420S1c7D1TTX0.0yes10.4163897.26919539.186101-69.26879924300.075.030518-29.699707242.553711-71.41113317.15478.2733624598.0799360.994396NaNNaNNaNNaNNaN8 mM-61.1738398.0
4OP23042023420003.abfS1823420S1c8D1TTX0.0yes10.4163896.00040031.599917-70.55053722350.081.011963-33.068848309.448242-61.40136716.65575.5139245786.9278981.182830NaNNaNNaNNaNNaN8 mM-60.9563508.0
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" + ], + "text/plain": [ + " OP filename slice cell_ch cell_ID day treatment \\\n", + "0 OP230420 23420003.abf S1 1 23420S1c1 D1 TTX \n", + "1 OP230420 23420003.abf S1 3 23420S1c3 D1 TTX \n", + "2 OP230420 23420003.abf S1 6 23420S1c6 D1 TTX \n", + "3 OP230420 23420003.abf S1 7 23420S1c7 D1 TTX \n", + "4 OP230420 23420003.abf S1 8 23420S1c8 D1 TTX \n", + "\n", + " hrs_incubation repatch hrs_after_OP Rs Rin \\\n", + "0 0.0 no 10.416389 6.675643 39.025301 \n", + "1 0.0 no 10.416389 7.867174 48.728367 \n", + "2 0.0 no 10.416389 8.820134 35.971082 \n", + "3 0.0 yes 10.416389 7.269195 39.186101 \n", + "4 0.0 yes 10.416389 6.000400 31.599917 \n", + "\n", + " resting_potential max_spikes Rheobase AP_heigth TH max_depol \\\n", + "0 -74.285889 24 200.0 80.749512 -35.278320 336.181641 \n", + "1 -69.573975 26 300.0 78.448486 -32.043457 350.097656 \n", + "2 -54.956055 22 300.0 76.660156 -29.827881 270.629883 \n", + "3 -69.268799 24 300.0 75.030518 -29.699707 242.553711 \n", + "4 -70.550537 22 350.0 81.011963 -33.068848 309.448242 \n", + "\n", + " max_repol membra_time_constant_tau capacitance comments rheo_ramp \\\n", + "0 -60.791016 19.40 510.601767 0 753.380113 \n", + "1 -67.138672 17.30 393.397918 1 585.102837 \n", + "2 -52.246094 14.85 426.098774 3 173.915797 \n", + "3 -71.411133 17.15 478.273362 4 598.079936 \n", + "4 -61.401367 16.65 575.513924 5 786.927898 \n", + "\n", + " AP_halfwidth Rheobse_ramp Unnamed: 27 rheos_ramp comment \\\n", + "0 1.151009 NaN NaN NaN NaN NaN \n", + "1 1.006321 NaN NaN NaN NaN NaN \n", + "2 1.266335 NaN NaN NaN NaN NaN \n", + "3 0.994396 NaN NaN NaN NaN NaN \n", + "4 1.182830 NaN NaN NaN NaN NaN \n", + "\n", + " high K concentration RMP_from_char K (mM) \n", + "0 8 mM -61.828554 8.0 \n", + "1 8 mM -60.460298 8.0 \n", + "2 8 mM -59.615979 8.0 \n", + "3 8 mM -61.173839 8.0 \n", + "4 8 mM -60.956350 8.0 " + ] + }, + "execution_count": 32, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df[\"K (mM)\"] = (df[\"high K concentration\"].str[:-2]).astype(float)\n", + "df.head()\n", + "\n" + ] }, { "cell_type": "code", @@ -219,7 +1406,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.3" + "version": "3.12.4" } }, "nbformat": 4,