{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# morar\n", "\n", "morar is a python package for working with tabular phenotypic screening data.\n", "\n", "### Example data\n", "\n", "This example data only has untreated (DMSO control) Cellprofiler measurements for three cell-lines (CPAP53, FLO1 & KYSE30)." ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "3115 rows \n", "175 columns\n" ] }, { "data": { "text/html": [ "
| \n", " | Metadata_compound | \n", "Metadata_concentration | \n", "Metadata_platename | \n", "Metadata_platenum | \n", "Metadata_site | \n", "Metadata_well | \n", "Cells_AreaShape_Area | \n", "Cells_AreaShape_Compactness | \n", "Cells_AreaShape_Eccentricity | \n", "Cells_AreaShape_Extent | \n", "... | \n", "Nuclei_Intensity_MaxIntensityEdge_W1 | \n", "Nuclei_Intensity_MaxIntensity_W1 | \n", "Nuclei_Intensity_MeanIntensityEdge_W1 | \n", "Nuclei_Intensity_MeanIntensity_W1 | \n", "Nuclei_Intensity_MedianIntensity_W1 | \n", "Nuclei_Intensity_MinIntensityEdge_W1 | \n", "Nuclei_Intensity_MinIntensity_W1 | \n", "Nuclei_Intensity_StdIntensityEdge_W1 | \n", "Nuclei_Intensity_StdIntensity_W1 | \n", "Nuclei_Intensity_UpperQuartileIntensity_W1 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "7313 | \n", "1.452288 | \n", "0.859793 | \n", "0.541102 | \n", "... | \n", "0.046601 | \n", "0.146944 | \n", "0.035183 | \n", "0.090561 | \n", "0.099413 | \n", "0.025620 | \n", "0.025620 | \n", "0.005066 | \n", "0.030142 | \n", "0.113756 | \n", "
| 1 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "6723 | \n", "1.045362 | \n", "0.542282 | \n", "0.673377 | \n", "... | \n", "0.035859 | \n", "0.171115 | \n", "0.022758 | \n", "0.094423 | \n", "0.106592 | \n", "0.017548 | \n", "0.017548 | \n", "0.003269 | \n", "0.045302 | \n", "0.133967 | \n", "
| 2 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "2545 | \n", "1.567167 | \n", "0.859639 | \n", "0.398216 | \n", "... | \n", "0.109331 | \n", "0.189944 | \n", "0.054827 | \n", "0.105230 | \n", "0.108217 | \n", "0.038651 | \n", "0.038651 | \n", "0.016095 | \n", "0.035619 | \n", "0.129328 | \n", "
| 3 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "5248 | \n", "2.244958 | \n", "0.968322 | \n", "0.711207 | \n", "... | \n", "0.029175 | \n", "0.164858 | \n", "0.021538 | \n", "0.087355 | \n", "0.095712 | \n", "0.017075 | \n", "0.017075 | \n", "0.002364 | \n", "0.043820 | \n", "0.125116 | \n", "
| 4 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "6290 | \n", "1.227357 | \n", "0.794636 | \n", "0.555850 | \n", "... | \n", "0.107851 | \n", "0.219272 | \n", "0.052124 | \n", "0.127815 | \n", "0.138277 | \n", "0.036500 | \n", "0.036500 | \n", "0.015603 | \n", "0.046839 | \n", "0.166781 | \n", "
5 rows × 175 columns
\n", "| \n", " | Cells_AreaShape_Area | \n", "Cells_AreaShape_Compactness | \n", "Cells_AreaShape_Eccentricity | \n", "Cells_AreaShape_Extent | \n", "Cells_AreaShape_FormFactor | \n", "Cells_AreaShape_MajorAxisLength | \n", "Cells_AreaShape_MaxFeretDiameter | \n", "Cells_AreaShape_MaximumRadius | \n", "Cells_AreaShape_MeanRadius | \n", "Cells_AreaShape_MedianRadius | \n", "... | \n", "Nuclei_Intensity_MaxIntensityEdge_W1 | \n", "Nuclei_Intensity_MaxIntensity_W1 | \n", "Nuclei_Intensity_MeanIntensityEdge_W1 | \n", "Nuclei_Intensity_MeanIntensity_W1 | \n", "Nuclei_Intensity_MedianIntensity_W1 | \n", "Nuclei_Intensity_MinIntensityEdge_W1 | \n", "Nuclei_Intensity_MinIntensity_W1 | \n", "Nuclei_Intensity_StdIntensityEdge_W1 | \n", "Nuclei_Intensity_StdIntensity_W1 | \n", "Nuclei_Intensity_UpperQuartileIntensity_W1 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "7313 | \n", "1.452288 | \n", "0.859793 | \n", "0.541102 | \n", "0.400085 | \n", "146.210894 | \n", "165.411608 | \n", "35.057096 | \n", "12.083201 | \n", "10.440307 | \n", "... | \n", "0.046601 | \n", "0.146944 | \n", "0.035183 | \n", "0.090561 | \n", "0.099413 | \n", "0.025620 | \n", "0.025620 | \n", "0.005066 | \n", "0.030142 | \n", "0.113756 | \n", "
| 1 | \n", "6723 | \n", "1.045362 | \n", "0.542282 | \n", "0.673377 | \n", "0.687665 | \n", "102.271033 | \n", "107.837841 | \n", "41.000000 | \n", "14.219288 | \n", "12.649111 | \n", "... | \n", "0.035859 | \n", "0.171115 | \n", "0.022758 | \n", "0.094423 | \n", "0.106592 | \n", "0.017548 | \n", "0.017548 | \n", "0.003269 | \n", "0.045302 | \n", "0.133967 | \n", "
| 2 | \n", "2545 | \n", "1.567167 | \n", "0.859639 | \n", "0.398216 | \n", "0.406467 | \n", "89.634503 | \n", "97.637083 | \n", "18.027756 | \n", "6.673246 | \n", "6.000000 | \n", "... | \n", "0.109331 | \n", "0.189944 | \n", "0.054827 | \n", "0.105230 | \n", "0.108217 | \n", "0.038651 | \n", "0.038651 | \n", "0.016095 | \n", "0.035619 | \n", "0.129328 | \n", "
| 3 | \n", "5248 | \n", "2.244958 | \n", "0.968322 | \n", "0.711207 | \n", "0.402723 | \n", "167.740973 | \n", "157.003185 | \n", "22.000000 | \n", "8.529908 | \n", "8.000000 | \n", "... | \n", "0.029175 | \n", "0.164858 | \n", "0.021538 | \n", "0.087355 | \n", "0.095712 | \n", "0.017075 | \n", "0.017075 | \n", "0.002364 | \n", "0.043820 | \n", "0.125116 | \n", "
| 4 | \n", "6290 | \n", "1.227357 | \n", "0.794636 | \n", "0.555850 | \n", "0.446626 | \n", "119.665209 | \n", "122.102416 | \n", "32.000000 | \n", "11.435842 | \n", "10.000000 | \n", "... | \n", "0.107851 | \n", "0.219272 | \n", "0.052124 | \n", "0.127815 | \n", "0.138277 | \n", "0.036500 | \n", "0.036500 | \n", "0.015603 | \n", "0.046839 | \n", "0.166781 | \n", "
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\n", "| \n", " | Metadata_compound | \n", "Metadata_concentration | \n", "Metadata_platename | \n", "Metadata_platenum | \n", "Metadata_site | \n", "Metadata_well | \n", "Cells_AreaShape_Area | \n", "Cells_AreaShape_Compactness | \n", "Cells_AreaShape_Eccentricity | \n", "Cells_AreaShape_Extent | \n", "... | \n", "Nuclei_Intensity_MaxIntensityEdge_W1 | \n", "Nuclei_Intensity_MaxIntensity_W1 | \n", "Nuclei_Intensity_MeanIntensityEdge_W1 | \n", "Nuclei_Intensity_MeanIntensity_W1 | \n", "Nuclei_Intensity_MedianIntensity_W1 | \n", "Nuclei_Intensity_MinIntensityEdge_W1 | \n", "Nuclei_Intensity_MinIntensity_W1 | \n", "Nuclei_Intensity_StdIntensityEdge_W1 | \n", "Nuclei_Intensity_StdIntensity_W1 | \n", "Nuclei_Intensity_UpperQuartileIntensity_W1 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "6659.5 | \n", "1.401312 | \n", "0.849465 | \n", "0.514216 | \n", "... | \n", "0.052392 | \n", "0.179820 | \n", "0.036169 | \n", "0.107214 | \n", "0.116831 | \n", "0.026741 | \n", "0.026741 | \n", "0.005556 | \n", "0.039872 | \n", "0.136389 | \n", "
| 1 | \n", "DMSO | \n", "0 | \n", "FLO1 | \n", "6116 | \n", "1 | \n", "A01 | \n", "7297.0 | \n", "1.180151 | \n", "0.744776 | \n", "0.566198 | \n", "... | \n", "0.073434 | \n", "0.317884 | \n", "0.050400 | \n", "0.167128 | \n", "0.172324 | \n", "0.035851 | \n", "0.035851 | \n", "0.007712 | \n", "0.069057 | \n", "0.221981 | \n", "
| 2 | \n", "DMSO | \n", "0 | \n", "KYSE30 | \n", "6114 | \n", "1 | \n", "A01 | \n", "5910.0 | \n", "1.352440 | \n", "0.806265 | \n", "0.513757 | \n", "... | \n", "0.011398 | \n", "0.012161 | \n", "0.009667 | \n", "0.009799 | \n", "0.009766 | \n", "0.008148 | \n", "0.007935 | \n", "0.000497 | \n", "0.000534 | \n", "0.010147 | \n", "
3 rows × 175 columns
\n", "| \n", " | Metadata_compound | \n", "Metadata_concentration | \n", "Metadata_platename | \n", "Metadata_platenum | \n", "Metadata_site | \n", "Metadata_well | \n", "Cells_AreaShape_Area | \n", "Cells_AreaShape_Compactness | \n", "Cells_AreaShape_Eccentricity | \n", "Cells_AreaShape_Extent | \n", "... | \n", "Nuclei_Intensity_MaxIntensityEdge_W1 | \n", "Nuclei_Intensity_MaxIntensity_W1 | \n", "Nuclei_Intensity_MeanIntensityEdge_W1 | \n", "Nuclei_Intensity_MeanIntensity_W1 | \n", "Nuclei_Intensity_MedianIntensity_W1 | \n", "Nuclei_Intensity_MinIntensityEdge_W1 | \n", "Nuclei_Intensity_MinIntensity_W1 | \n", "Nuclei_Intensity_StdIntensityEdge_W1 | \n", "Nuclei_Intensity_StdIntensity_W1 | \n", "Nuclei_Intensity_UpperQuartileIntensity_W1 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "6924.574271 | \n", "1.658188 | \n", "0.812143 | \n", "0.500624 | \n", "... | \n", "0.052693 | \n", "0.178927 | \n", "0.035780 | \n", "0.102651 | \n", "0.111341 | \n", "0.025760 | \n", "0.025755 | \n", "0.005930 | \n", "0.040513 | \n", "0.134633 | \n", "
| 1 | \n", "DMSO | \n", "0 | \n", "FLO1 | \n", "6116 | \n", "1 | \n", "A01 | \n", "8380.209003 | \n", "1.250192 | \n", "0.721066 | \n", "0.577295 | \n", "... | \n", "0.085844 | \n", "0.327951 | \n", "0.051686 | \n", "0.168493 | \n", "0.172363 | \n", "0.036072 | \n", "0.036071 | \n", "0.011810 | \n", "0.074594 | \n", "0.227802 | \n", "
| 2 | \n", "DMSO | \n", "0 | \n", "KYSE30 | \n", "6114 | \n", "1 | \n", "A01 | \n", "10470.664175 | \n", "1.484766 | \n", "0.770031 | \n", "0.513447 | \n", "... | \n", "0.013575 | \n", "0.015417 | \n", "0.011248 | \n", "0.011733 | \n", "0.011744 | \n", "0.009092 | \n", "0.008876 | \n", "0.000881 | \n", "0.001034 | \n", "0.012416 | \n", "
3 rows × 175 columns
\n", "| \n", " | PC1 | \n", "PC2 | \n", "PC3 | \n", "PC4 | \n", "PC5 | \n", "PC6 | \n", "PC7 | \n", "PC8 | \n", "PC9 | \n", "PC10 | \n", "... | \n", "PC160 | \n", "PC161 | \n", "PC162 | \n", "PC163 | \n", "Metadata_compound | \n", "Metadata_concentration | \n", "Metadata_platename | \n", "Metadata_platenum | \n", "Metadata_site | \n", "Metadata_well | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "0.892394 | \n", "-5.027810 | \n", "1.848411 | \n", "-0.844165 | \n", "0.453647 | \n", "0.111056 | \n", "0.509544 | \n", "-1.760124 | \n", "1.689087 | \n", "3.040456 | \n", "... | \n", "-0.000450 | \n", "0.002858 | \n", "-0.003976 | \n", "0.002758 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "
| 1 | \n", "1.532934 | \n", "-5.931854 | \n", "2.057423 | \n", "-2.275006 | \n", "0.930320 | \n", "0.783315 | \n", "1.259424 | \n", "1.488056 | \n", "-0.534312 | \n", "1.826376 | \n", "... | \n", "0.001523 | \n", "-0.002552 | \n", "0.000463 | \n", "-0.003439 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "
| 2 | \n", "4.913065 | \n", "-2.134422 | \n", "-2.722417 | \n", "5.353066 | \n", "-1.349470 | \n", "2.371191 | \n", "-0.451264 | \n", "-1.268996 | \n", "-4.387346 | \n", "-0.169706 | \n", "... | \n", "-0.003100 | \n", "-0.002865 | \n", "-0.001382 | \n", "-0.003420 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "
| 3 | \n", "0.924419 | \n", "-6.267590 | \n", "1.299768 | \n", "1.443804 | \n", "0.443817 | \n", "-2.715458 | \n", "3.595639 | \n", "-0.919689 | \n", "0.265012 | \n", "0.140926 | \n", "... | \n", "0.001229 | \n", "0.009523 | \n", "-0.001668 | \n", "-0.000444 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "
| 4 | \n", "6.063763 | \n", "-2.678332 | \n", "0.144865 | \n", "2.995934 | \n", "-0.326641 | \n", "2.347589 | \n", "0.425272 | \n", "-3.152036 | \n", "-3.636349 | \n", "-1.353622 | \n", "... | \n", "-0.003887 | \n", "-0.012992 | \n", "0.002697 | \n", "0.006550 | \n", "DMSO | \n", "0 | \n", "CPAP53 | \n", "6119 | \n", "1 | \n", "A01 | \n", "
5 rows × 169 columns
\n", "