| Next changeset 1:81f9b44f5242 (2017-02-27) |
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Commit message:
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run_flock/runFlockMFI.py run_flock/runFlockMFI.xml run_flock/static/images/flock_logo.png run_flock/test-data/input.flowtext run_flock/test-data/mfi.flowmfi run_flock/test-data/mfi2.flowmfi run_flock/test-data/mfi3.flowmfi run_flock/test-data/out1.flowclr run_flock/test-data/out1.flowscore run_flock/test-data/out2.flowclr run_flock/test-data/out2.flowscore run_flock/test-data/out3.flowclr run_flock/test-data/out3.flowscore |
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| diff -r 000000000000 -r c1e924e37080 run_flock/runFlockMFI.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/runFlockMFI.py Mon Feb 27 13:06:23 2017 -0500 |
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| @@ -0,0 +1,125 @@ +#!/usr/bin/env python +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +# version 2 +from __future__ import print_function + +import sys +import os +from argparse import ArgumentParser +import pandas as pd +from scipy.stats import gmean + + +def run_FLOCK(input_file, method, bins, density, output_file, mfi_file, + mfi_calc, profile, tool_directory): + run_command = tool_directory + "/bin/" + method + " " + input_file + if bins: + run_command += " " + bins + if density: + run_command += " " + density + + os.system(run_command) + + move_command = "mv flock_results.txt " + output_file + os.system(move_command) + + # Here add some way to calculate the count and tack it on to profile file. + flockdf = pd.read_table(output_file) + if mfi_calc == "mfi": + MFIs = flockdf.groupby('Population').mean().round(decimals=2) + elif mfi_calc == "gmfi": + MFIs = flockdf.groupby('Population').agg(lambda x: gmean(list(x))).round(decimals=2) + else: + MFIs = flockdf.groupby('Population').median().round(decimals=2) + + with open(mfi_file, "w") as outf: + MFIs.to_csv(outf, sep="\t", float_format='%.0f') + + (events, columns) = flockdf.shape + fstats = {} + fstats['population'] = flockdf.iloc[:, -1:].iloc[:, 0] + fstats['population_freq'] = fstats['population'].value_counts() + fstats['population_freq_sort'] = fstats['population_freq'].sort_index() + fstats['population_per'] = (fstats['population'].value_counts(normalize=True) * 100).round(decimals=2) + fstats['population_per_sort'] = fstats['population_per'].sort_index() + fstats['population_all'] = pd.concat([fstats['population_freq_sort'], fstats['population_per_sort']], axis=1) + fstats['population_all'].columns = ['Count', 'Percentage'] + fstats['population_all']['Population_ID'] = fstats['population_all'].index + + flock_profile = pd.read_table('profile.txt') + profile_pop = flock_profile.merge(fstats['population_all'], on='Population_ID') + profile_pop.to_csv(profile, sep="\t", float_format='%.2f', index=False) + +# get_profile = "mv profile.txt " + profile +# os.system(get_profile) + return + + +if __name__ == "__main__": + parser = ArgumentParser( + prog="runFlockMFI", + description="Run Flock on text file and generate centroid file") + + parser.add_argument( + '-i', + dest="input_file", + required=True, + help="File location for the FCS file.") + + parser.add_argument( + '-m', + dest="method", + required=True, + help="Run flock1 or flock2.") + + parser.add_argument( + '-M', + dest="mfi_calc", + required=True, + help="what to calculate for centroids.") + + parser.add_argument( + '-b', + dest="bins", + required=False, + help="Number of Bins.") + + parser.add_argument( + '-d', + dest="density", + required=False, + help="Density.") + + parser.add_argument( + '-o', + dest="output_file", + required=True, + help="File location for the output file.") + + parser.add_argument( + '-t', + dest="tool_directory", + required=True, + help="File location for the output file.") + + parser.add_argument( + '-c', + dest="centroids", + required=True, + help="File location for the output centroid file.") + + parser.add_argument( + '-p', + dest="profile", + required=True, + help="File location for the output profile file.") + + args = parser.parse_args() + run_FLOCK(args.input_file, args.method, args.bins, + args.density, args.output_file, args.centroids, args.mfi_calc, + args.profile, args.tool_directory) + + sys.exit(0) |
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| diff -r 000000000000 -r c1e924e37080 run_flock/runFlockMFI.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/runFlockMFI.xml Mon Feb 27 13:06:23 2017 -0500 |
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| @@ -0,0 +1,158 @@ +<tool id="run_flock" name="Run FLOCK" version="1.2"> + <description>using a FCS file that was converted/transformed to a text file.</description> + <requirements> + <requirement type="package" version="0.16.0">scipy</requirement> + <requirement type="package" version="0.17.1">pandas</requirement> + <requirement type="package" version="1.0">flock</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python $__tool_directory__/runFlockMFI.py -i "${input}" -o "${output}" -m "${method}" -c "${centroid}" -M "${mfi}" -p "${profile}" -t $__tool_directory__ + #if $bins + -b $bins + #end if + #if $density + -d $density + #end if + ]]> + </command> + <inputs> + <param format="flowtext" name="input" type="data" label="Source file"/> + <param name="method" type="select" label="Method"> + <option value="flock1" selected="true">Flock Version 1</option> + <option value="flock2">Flock Version 2</option> + </param> + <param name="bins" type="integer" min="6" max="30" optional="true" value="" label="bins (6-30)"/> + <param name="density" type="integer" min="2" max="100" optional="true" value="" label="density (2-100)"/> + <param name="mfi" type="select" label="Calculate centroids using:"> + <option value="mfi" selected="true">Mean Fluorescence Intensity</option> + <option value="mdfi">Median Fluorescence Intensity</option> + <option value="gmfi">Geometric Mean Fluorescence Intensity</option> + </param> + </inputs> + <outputs> + <data format="flowclr" name="output" label="${method} with ${mfi} on ${input.name}"/> + <data format="flowmfi" name="centroid" label="${mfi} centroids from ${method} on ${input.name}"/> + <data format="flowscore" name="profile" label="Population score profiles from ${method} on ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="input.flowtext"/> + <param name="method" value="flock1"/> + <param name="bins" value=""/> + <param name="density" value=""/> + <param name="mfi" value="mfi"/> + <output name="output" file="out1.flowclr"/> + <output name="centroid" file="mfi.flowmfi"/> + <output name="profile" file="out1.flowscore"/> + </test> + <test> + <param name="input" value="input.flowtext"/> + <param name="method" value="flock2"/> + <param name="bins" value=""/> + <param name="density" value=""/> + <param name="mfi" value="mfi"/> + <output name="output" file="out2.flowclr"/> + <output name="centroid" file="mfi2.flowmfi"/> + <output name="profile" file="out2.flowscore"/> + </test> + <test> + <param name="input" value="input.flowtext"/> + <param name="method" value="flock1"/> + <param name="bins" value="7"/> + <param name="density" value="3"/> + <param name="mfi" value="mfi"/> + <output name="output" file="out3.flowclr"/> + <output name="centroid" file="mfi3.flowmfi"/> + <output name="profile" file="out3.flowscore"/> + </test> + </tests> + <help><![CDATA[ + This tool runs FLOCK using a FCS file that was converted to a text file. + +----- + +.. image:: static/images/flowtools/flock_logo.png + +FLOCK (FLOw Clustering without K) is a computational approach to flow cytometry analysis which: + + 1. Computationally determines the number of unique populations in high dimensional flow data using a rapid binning approach + 2. Can handle non-spherical hyper-shapes + 3. Maps populations across independent samples + 4. Calculates many useful summary statistics + 5. Finds the most informative parameters + 6. Reduces subjective factors in manual gating + +.. class:: warningmark + +This tool is not intended to analyze CyTOF data as is. + +----- + +**Input** + +FLOCK requires a text file, generated from a FCS file, as input. +In order to define the populations in a given dataset collection for a given set of markers, run FLOCK on a super-set of FCS file. Use the Downsample and merge tool to concatenate and/or downsample datasets, and remove, edit or rearrange markers before running FLOCK on your favorite set of markers. + +**Output** + +*FLOCK* + +FLOCK attributes each event to a population and generates a text file. + +*Centroids* + +The centroid file is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population defined by FLOCK, as determined by the user. + +*Population scores* + +This output is a table containing marker scores for each population. The score value is a number indicating the degree to which this population expresses each marker, as follows: + +- 1 implies negative expression +- 2 implies low expression +- 3 implies positive expression +- 4 implies highly positive expression + +----- + +**Example** + +*Input* - fluorescence intensities per marker per event:: + + Marker1 Marker2 Marker3 + 34 45 12 + 33 65 10 + 19 62 98 + 12 36 58 + +*FLOCK Output* - fluorescence intensities per marker and population ID per event:: + + Marker1 Marker2 Marker3 Population + 34 45 12 1 + 33 65 10 5 + 19 62 98 2 + 12 36 58 1 + +*Centroid file* - mean, geometric mean or median fluorescence intensity per marker per population:: + + Population Marker1 Marker2 Marker3 + 1 38 49 10 + 2 21 63 100 + 3 31 52 45 + 4 11 78 25 + +*Population profile file*:: + + Population_ID Marker1 Marker2 Marker3 Count Percentage + 1 1 3 2 3885 6.44 + 2 1 3 4 2774 4.62 + 3 2 2 3 2151 3.59 + 4 1 3 2 1207 2.01 + ]]> + </help> + <citations> + <citation type="doi">10.1002/cyto.b.20554</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/input.flowtext --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/input.flowtext Mon Feb 27 13:06:23 2017 -0500 |
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\n' |
| b |
| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/mfi.flowmfi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/mfi.flowmfi Mon Feb 27 13:06:23 2017 -0500 |
| b |
| @@ -0,0 +1,31 @@ +Population FSC SSC CD4 CCR3 CD8 CCR7 +1 357 117 517 12 57 111 +2 333 152 69 20 69 106 +3 355 174 76 152 79 77 +4 421 381 147 402 140 186 +5 372 124 524 227 51 131 +6 370 150 75 26 618 264 +7 358 118 513 119 57 114 +8 378 207 99 127 120 218 +9 360 121 518 179 51 38 +10 384 158 83 154 620 272 +11 367 152 70 98 583 164 +12 414 146 527 208 71 282 +13 374 126 520 150 57 196 +14 387 184 91 96 338 101 +15 355 118 515 27 58 34 +16 369 124 516 20 70 188 +17 411 147 530 41 86 301 +18 675 453 385 196 184 256 +19 613 988 153 256 222 257 +20 620 986 151 255 224 180 +21 745 1015 190 274 255 261 +22 655 987 153 244 224 70 +23 540 926 347 485 363 413 +24 766 1012 181 267 243 163 +25 966 965 328 323 295 331 +26 650 392 384 179 171 121 +27 612 965 145 152 213 228 +28 578 934 128 172 209 129 +29 979 1010 437 523 406 456 +30 749 858 535 834 564 580 |
| b |
| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/mfi2.flowmfi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/mfi2.flowmfi Mon Feb 27 13:06:23 2017 -0500 |
| b |
| @@ -0,0 +1,15 @@ +Population FSC SSC CD4 CCR3 CD8 CCR7 +1 367 123 521 108 59 131 +2 360 183 77 104 121 127 +3 375 154 77 95 610 244 +4 361 129 289 89 84 93 +5 648 399 415 19 173 207 +6 695 472 397 233 188 255 +7 659 980 162 242 229 197 +8 442 383 325 616 334 397 +9 651 402 390 178 171 142 +10 574 983 351 479 362 412 +11 493 634 496 864 562 577 +12 509 341 169 224 161 383 +13 1007 976 326 320 298 306 +14 996 1013 454 536 426 469 |
| b |
| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/mfi3.flowmfi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/mfi3.flowmfi Mon Feb 27 13:06:23 2017 -0500 |
| b |
| @@ -0,0 +1,10 @@ +Population FSC SSC CD4 CCR3 CD8 CCR7 +1 375 155 78 95 607 244 +2 366 123 519 189 53 95 +3 357 178 79 99 116 124 +4 387 132 522 110 67 234 +5 653 422 372 195 177 212 +6 357 118 513 28 60 95 +7 630 966 148 227 219 135 +8 724 937 380 497 376 426 +9 694 997 177 257 239 247 |
| b |
| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/out1.flowclr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/out1.flowclr Mon Feb 27 13:06:23 2017 -0500 |
| b |
| b'@@ -0,0 +1,20000 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\n+637\t1023\t203\t289\t255\t175\t20\n+649\t902\t155\t165\t213\t262\t27\n+322\t148\t0\t187\t87\t115\t3\n' |
| b |
| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/out1.flowscore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/out1.flowscore Mon Feb 27 13:06:23 2017 -0500 |
| b |
| @@ -0,0 +1,31 @@ +Population_ID FSC SSC CD4 CCR3 CD8 CCR7 Count Percentage +1 1 1 3 1 1 1 1093 5.47 +2 1 1 1 1 1 1 695 3.48 +3 1 1 1 1 1 1 574 2.87 +4 1 2 1 2 1 1 146 0.73 +5 1 1 3 1 1 1 982 4.91 +6 1 1 1 1 3 2 1212 6.06 +7 1 1 3 1 1 1 1055 5.28 +8 1 1 1 1 1 1 578 2.89 +9 1 1 3 1 1 1 986 4.93 +10 1 1 1 1 3 2 1326 6.63 +11 1 1 1 1 3 1 693 3.47 +12 1 1 3 1 1 2 368 1.84 +13 1 1 3 1 1 1 841 4.21 +14 1 1 1 1 2 1 315 1.58 +15 1 1 3 1 1 1 879 4.40 +16 1 1 3 1 1 1 911 4.56 +17 1 1 3 1 1 2 323 1.62 +18 3 2 3 1 1 2 522 2.61 +19 2 4 1 1 1 2 1003 5.02 +20 2 4 1 1 1 1 1081 5.41 +21 3 4 1 2 2 2 947 4.74 +22 3 4 1 1 1 1 597 2.99 +23 2 4 2 2 2 3 297 1.49 +24 3 4 1 2 1 1 699 3.50 +25 4 4 2 2 2 2 289 1.45 +26 3 2 3 1 1 1 364 1.82 +27 2 4 1 1 1 2 586 2.93 +28 2 4 1 1 1 1 485 2.43 +29 4 4 3 2 2 3 106 0.53 +30 4 4 3 4 2 3 46 0.23 |
| b |
| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/out2.flowclr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/out2.flowclr Mon Feb 27 13:06:23 2017 -0500 |
| b |
| b'@@ -0,0 +1,20000 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255\t159\t220\t7\n+608\t1023\t115\t247\t174\t266\t7\n+637\t1023\t203\t289\t255\t175\t7\n+649\t902\t155\t165\t213\t262\t7\n+322\t148\t0\t187\t87\t115\t2\n' |
| b |
| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/out2.flowscore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/out2.flowscore Mon Feb 27 13:06:23 2017 -0500 |
| b |
| @@ -0,0 +1,15 @@ +Population_ID FSC SSC CD4 CCR3 CD8 CCR7 Count Percentage +1 1 1 3 1 1 1 7351 36.76 +2 1 1 1 1 1 1 2126 10.63 +3 1 1 1 1 3 2 3264 16.32 +4 1 1 2 1 1 1 148 0.74 +5 2 2 3 1 1 2 88 0.44 +6 3 2 3 1 1 2 366 1.83 +7 3 4 1 1 1 1 5562 27.81 +8 1 2 2 3 2 3 37 0.19 +9 3 2 3 1 1 1 398 1.99 +10 2 4 2 2 2 2 292 1.46 +11 2 2 3 4 2 3 14 0.07 +12 2 2 1 1 1 2 40 0.20 +13 4 4 2 2 2 2 157 0.79 +14 4 4 3 2 2 3 156 0.78 |
| b |
| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/out3.flowclr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/out3.flowclr Mon Feb 27 13:06:23 2017 -0500 |
| b |
| b'@@ -0,0 +1,20000 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7\t255\t159\t220\t9\n+608\t1023\t115\t247\t174\t266\t9\n+637\t1023\t203\t289\t255\t175\t7\n+649\t902\t155\t165\t213\t262\t9\n+322\t148\t0\t187\t87\t115\t3\n' |
| b |
| diff -r 000000000000 -r c1e924e37080 run_flock/test-data/out3.flowscore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_flock/test-data/out3.flowscore Mon Feb 27 13:06:23 2017 -0500 |
| b |
| @@ -0,0 +1,10 @@ +Population_ID FSC SSC CD4 CCR3 CD8 CCR7 Count Percentage +1 1 1 1 1 3 2 3297 16.49 +2 1 1 3 1 1 1 2695 13.48 +3 1 1 1 1 1 1 2094 10.47 +4 1 1 3 1 1 2 1932 9.66 +5 3 2 3 1 1 2 934 4.67 +6 1 1 3 1 1 1 2852 14.26 +7 2 4 1 1 1 1 2478 12.39 +8 4 4 2 2 2 3 568 2.84 +9 3 4 1 2 1 2 3149 15.75 |
