diff --git a/01_flow_cytometry/exercises.m b/01_flow_cytometry/exercises.m index 6984a31..4114242 100644 --- a/01_flow_cytometry/exercises.m +++ b/01_flow_cytometry/exercises.m @@ -15,10 +15,10 @@ % Examples of flow data (Fig1 to Fig4) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % pure scatter - often hard to interpret -fcs_scatter([dosedata 'LacI-CAGop_C4_C04_P3.fcs'],'PE-Tx-Red-YG-A','Pacific Blue-A',0,[0 0; 6 6],1); % Fig1 +fcs_scatter([dosedata 'LacI-CAGop_C4_P3.fcs'],'PE-Tx-Red-YG-A','Pacific Blue-A',0,[0 0; 6 6],1); % Fig1 fcs_scatter([colordata '07-29-11_EYFP_P3.fcs'],'FITC-A','Pacific Blue-A',0,[0 0; 6 6],1); % Fig2 % smoothed density plot omits details but often summarizes collective better -data1 = fcs_scatter([dosedata 'LacI-CAGop_C4_C04_P3.fcs'],'PE-Tx-Red-YG-A','Pacific Blue-A',1,[0 0; 6 6],1); % Fig3 +data1 = fcs_scatter([dosedata 'LacI-CAGop_C4_P3.fcs'],'PE-Tx-Red-YG-A','Pacific Blue-A',1,[0 0; 6 6],1); % Fig3 data2 = fcs_scatter([colordata '07-29-11_EYFP_P3.fcs'],'FITC-A','Pacific Blue-A',1,[0 0; 6 6],1); % Fig4 % Things to notice: @@ -82,7 +82,7 @@ filtered = read_filtered_au(CM,[colordata '07-29-11_EYFP_P3.fcs']); % applies any filters set in ColorModel CM = set_dequantization(CM,true); % dequantization adds noise to spread the data out more, especially useful at low levels -[dequantized hdr] = read_filtered_au(CM,[dosedata 'LacI-CAGop_C4_C04_P3.fcs']); +[dequantized hdr] = read_filtered_au(CM,[dosedata 'LacI-CAGop_C4_P3.fcs']); xc = dequantized(:,10); yc = dequantized(:,11); pos = xc>0 & yc>0; figure; smoothhist2D(log10([xc(pos) yc(pos)]),10,[200, 200],[],'image',[0 0; 6 6]); % Fig5 diff --git a/02_flow_compensation/exercises.m b/02_flow_compensation/exercises.m index 508e216..571ee1f 100644 --- a/02_flow_compensation/exercises.m +++ b/02_flow_compensation/exercises.m @@ -114,8 +114,8 @@ CM = set_ERF_channel_name(CM, 'FITC-A'); % We'll explain this in the next exercise % Now let's read some files... -raw = read_filtered_au(CM,[dosedata 'LacI-CAGop_C3_C03_P3.fcs']); -compensated = readfcs_compensated_au(CM,[dosedata 'LacI-CAGop_C3_C03_P3.fcs'],0,1); +raw = read_filtered_au(CM,[dosedata 'LacI-CAGop_C3_P3.fcs']); +compensated = readfcs_compensated_au(CM,[dosedata 'LacI-CAGop_C3_P3.fcs'],0,1); % You should see an error: need to "resolve" the color model first! Comment % out above line of code and run again. @@ -159,7 +159,7 @@ % even when it can be compensated for. -compensated = readfcs_compensated_au(CM,[dosedata 'LacI-CAGop_C3_C03_P3.fcs'],0,1); +compensated = readfcs_compensated_au(CM,[dosedata 'LacI-CAGop_C3_P3.fcs'],0,1); % The last two arguments are: % 1) Whether to add autofluorescence back in after reading (generally not done) % 2) Whether to map all values <= 0 to 1 (which is zero on the log scale) diff --git a/Excel_README.md b/Excel_README.md new file mode 100644 index 0000000..4efa4c9 --- /dev/null +++ b/Excel_README.md @@ -0,0 +1,57 @@ +# TASBE Flow Analytics Excel Interface Instruction Guide + +A new feature of the TASBE Flow Analytics package is an Excel interface that provides a user-friendly interface between raw FCS data and current TASBE data analysis tools. Using a template spreadsheet, scientists can document important aspects of their experiments without having to worry about writing Matlab code. Currently, the template is organized into 6 sheets: +* "Experiment": includes all of the general experiment information and filename templates +* "Samples": includes important information regarding samples and batch analysis +* "Calibration": includes information to generate a Color Model +* "Comparative Analysis": includes information to run plusminus analysis +* "Transfer Curve Analysis": includes information to run transfer curve analysis +* "Optional Settings": TASBEConfig preferences that should not be changed unless absolutely necessary + +**Note**: All filepaths are relative to the location of the spreadsheet template unless they are absolute paths. + +## User Instructions +An example of the template is located in the TASBEFlowAnalytics-Tutorial titled ```batch_template.xlsm```. This example spreadsheet uses the tutorial +FCS data. The code needed to run the template is in the TASBEFlowAnalytics [coverney.excel](https://github.com/TASBE/TASBEFlowAnalytics/tree/coverney.excel) branch. The following sections describe specific features for each template sheet. There are more notes highlighted in green throughout the spreadsheet. + +### Experiment +* Filename templates are used to generate the correct FCS filenames without having to type all of them out. Each filename template is separated into numbered sections with some sections being static and some being variable. The variable sections must correspond to column names in "Samples". +(i.e. A template of 1_2_3.fcs would have the numbers replaced with the three correct inputs.) **Make sure to update the blueprint of number placeholders right below the Filename Template header.** +* The conditions keys are used to make sure that the values for a certain column name in "Samples" is valid. The keys are used to obtain the sets for plusminus analysis. + +### Samples +* The Sample Name column is necessary for the analysis and needs to be manually filled out. +* Information for each replicate should be in the same row with commas separating the values (i.e. sample locations for three replicates could look like A1,A2,A3). This feature is not applicable to the experimental condition columns. +* The "Update Filenames" button serves to generate sample filenames using the filename templates. These filenames are used in the TASBE ```getExcelFilename``` function, so it is important to click the "Update Filenames" button before running any analyses procedures. +* "Statistics Filename", "Statistics Filepath", "Point Cloud Filename", and "Point Cloud Filepath" are preferences for batch analysis. "Point Cloud Filename" takes in a filename template number instead of a string name since Point Cloud files are generated for multiple samples. + +### Calibration +* Multiple bead files can be compared by listing out their sample names in the "Sample Name" cell within the "Rainbow Beads" section. (i.e. Beads,Beads2,Beads3). The "Bead Comparison Tolerance" determines how identical you want the bead files to be. The results of the comparisons will be included in the TASBESession located at the bottom of the sheet. +* The "Constitutive/Input/Output" cells within the "Fluorochromes" section are optional for batch analysis but required for plusminus and transfer curve analysis. If this feature will be used, exactly one channel must be marked as Constitutive. The minimum is 2 colors with the second color acting as both the input and output. (It only needs to be labeled as one of the two.) For 3 or more colors, all pairwise combinations between labeled inputs and outputs will be analyzed. Colors not labeled will be ignored. +* The "Relevant Channels" cell within the "Color Translation" section determines which colors to consider when creating the Color Model. A value of "all" means all listed colors will be used. + +### Comparative Analysis +* "Comparison Group(s)" contains sample column name-value pairs that determine which samples in the "Samples" sheet are compared. +* "Comparisons" consist of the required primary comparison sets (i.e. +,-) and the secondary ordering inductions, which are optional. Both the primary and secondary sets are in the form of sample column names for a single plusminus analysis. +* Multiple plusminus analysis can be run as long as the Comparison Groups are aligned with their respective Comparison values. Additional preferences including otuput filename and plot path are required for each analysis. +* The "End Row Number" cell is currently required in order to determine the relative position of the generic plusminus preferences. The value should correspond to the last row (yellow fill) in Comparison Groups/Comparisons. +* The stem and device name cells were removed and replaced by automatically generated condition names in the format of "column name = value" for each Comparison Group. + +### Transfer Curve Analysis +* "Comparison Group(s)" contains sample column name-value pairs that determine which samples in the "Samples" sheet are analyzed. Each pair should correspond to a value in "Comparisons". +* "Comparisons" consists of the sample column name with the transfer curve conditions. It is important for the values to be numerical. Additional preferences including stem name and plot path are required for each analysis. +* Device name cells were removed. The defaults for stem names are in the format of "column name = value" for each Comparison Group, or they are the experiment name. + +### Optional Settings +* To change a preference, input the new value within the Value column. +* MEFL-converted point clouds can be obtained by setting the value of the "flow.outputPointCloud" preference to 1. + +### Next Steps +**Before running TASBEFlowAnalytics, make sure you have installed TASBE and are not just running it from the directory. Installation instructions are located in the TASBEFlowAnalytics [README](https://github.com/TASBE/TASBEFlowAnalytics/blob/develop/README.md).** + +After completing and saving the template spreadsheet, the actual analysis can be run in two ways: +1) Run the function ```analyzeFromExcel``` (located in the code directory of TASBEFlowAnalytics) +with the file path of the spreadsheet as the input and the type ('colormodel', 'batch', 'plusminus', or 'transfercurve'). ```analyzeFromExcel``` will then create a TemplateExtraction object and run the correct analysis. +2) Click the run buttons located in each sheet of the template. From there, ```analyzeFromExcel``` is automatically called with the correct inputs. The TASBESession log would then be outputted near the bottom of the relevant sheet. The template contains some more detailed instructions to set up the buttons. **This feature currently only works with Windows.** + +**Note**: The code is based on the coordinates of several important variables. You can adjust those coordinates accordingly using the ```setExcelCoordinates``` function within the ```TemplateExtraction``` class. diff --git a/batch_template.xlsm b/batch_template.xlsm new file mode 100644 index 0000000..bd0ae35 Binary files /dev/null and b/batch_template.xlsm differ diff --git a/example_assay/LacI-CAGop_B10_B10_P3.fcs b/example_assay/LacI-CAGop_B10_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B10_B10_P3.fcs rename to example_assay/LacI-CAGop_B10_P3.fcs diff --git a/example_assay/LacI-CAGop_B11_B11_P3.fcs b/example_assay/LacI-CAGop_B11_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B11_B11_P3.fcs rename to example_assay/LacI-CAGop_B11_P3.fcs diff --git a/example_assay/LacI-CAGop_B12_B12_P3.fcs b/example_assay/LacI-CAGop_B12_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B12_B12_P3.fcs rename to example_assay/LacI-CAGop_B12_P3.fcs diff --git a/example_assay/LacI-CAGop_B3_B03_P3.fcs b/example_assay/LacI-CAGop_B3_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B3_B03_P3.fcs rename to example_assay/LacI-CAGop_B3_P3.fcs diff --git a/example_assay/LacI-CAGop_B4_B04_P3.fcs b/example_assay/LacI-CAGop_B4_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B4_B04_P3.fcs rename to example_assay/LacI-CAGop_B4_P3.fcs diff --git a/example_assay/LacI-CAGop_B5_B05_P3.fcs b/example_assay/LacI-CAGop_B5_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B5_B05_P3.fcs rename to example_assay/LacI-CAGop_B5_P3.fcs diff --git a/example_assay/LacI-CAGop_B6_B06_P3.fcs b/example_assay/LacI-CAGop_B6_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B6_B06_P3.fcs rename to example_assay/LacI-CAGop_B6_P3.fcs diff --git a/example_assay/LacI-CAGop_B7_B07_P3.fcs b/example_assay/LacI-CAGop_B7_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B7_B07_P3.fcs rename to example_assay/LacI-CAGop_B7_P3.fcs diff --git a/example_assay/LacI-CAGop_B8_B08_P3.fcs b/example_assay/LacI-CAGop_B8_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B8_B08_P3.fcs rename to example_assay/LacI-CAGop_B8_P3.fcs diff --git a/example_assay/LacI-CAGop_B9_B09_P3.fcs b/example_assay/LacI-CAGop_B9_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_B9_B09_P3.fcs rename to example_assay/LacI-CAGop_B9_P3.fcs diff --git a/example_assay/LacI-CAGop_C1_C01_P3.fcs b/example_assay/LacI-CAGop_C1_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_C1_C01_P3.fcs rename to example_assay/LacI-CAGop_C1_P3.fcs diff --git a/example_assay/LacI-CAGop_C2_C02_P3.fcs b/example_assay/LacI-CAGop_C2_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_C2_C02_P3.fcs rename to example_assay/LacI-CAGop_C2_P3.fcs diff --git a/example_assay/LacI-CAGop_C3_C03_P3.fcs b/example_assay/LacI-CAGop_C3_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_C3_C03_P3.fcs rename to example_assay/LacI-CAGop_C3_P3.fcs diff --git a/example_assay/LacI-CAGop_C4_C04_P3.fcs b/example_assay/LacI-CAGop_C4_P3.fcs similarity index 100% rename from example_assay/LacI-CAGop_C4_C04_P3.fcs rename to example_assay/LacI-CAGop_C4_P3.fcs diff --git a/example_assay/LacI-Hef1a-mkate_A3_A03_P3.fcs b/example_assay/LacI-Hef1a-mkate_A3_P3.fcs similarity index 100% rename from example_assay/LacI-Hef1a-mkate_A3_A03_P3.fcs rename to example_assay/LacI-Hef1a-mkate_A3_P3.fcs diff --git a/example_controls/2012-03-12_Beads2_P3.fcs b/example_controls/2012-03-12_Beads2_P3.fcs new file mode 100644 index 0000000..432de2a Binary files /dev/null and b/example_controls/2012-03-12_Beads2_P3.fcs differ diff --git a/template_analysis/LacI-CAGop-Fine.mat b/template_analysis/LacI-CAGop-Fine.mat index fc674fa..be6b90c 100644 Binary files a/template_analysis/LacI-CAGop-Fine.mat and b/template_analysis/LacI-CAGop-Fine.mat differ diff --git a/template_analysis/LacI-CAGop-batch.csv b/template_analysis/LacI-CAGop-batch.csv deleted file mode 100644 index d8f8572..0000000 --- a/template_analysis/LacI-CAGop-batch.csv +++ /dev/null @@ -1,16 +0,0 @@ -Device Id,datapoints,,,log10 Mean,,,Std.Dev. of mean (fold) -,EBFP2,EYFP,mKate,EBFP2,EYFP,mKate,EBFP2,EYFP,mKate -Dox 0.1,52482,109175,119351,4.345084e+00,5.394359e+00,5.609663e+00,1,1,1, -Dox 0.2,42682,88230,95559,4.344227e+00,5.391166e+00,5.606492e+00,1,1,1, -Dox 0.5,40799,85195,92821,4.342561e+00,5.406055e+00,5.622935e+00,1,1,1, -Dox 1.0,35745,74814,81622,4.340866e+00,5.406947e+00,5.630341e+00,1,1,1, -Dox 2.0,39959,83476,91641,4.342808e+00,5.395057e+00,5.628313e+00,1,1,1, -Dox 5.0,47149,97621,108001,4.348411e+00,5.390884e+00,5.627314e+00,1,1,1, -Dox 10.0,44674,91712,100259,4.351312e+00,5.401429e+00,5.622702e+00,1,1,1, -Dox 20.0,48738,95318,104607,4.393307e+00,5.406043e+00,5.639542e+00,1,1,1, -Dox 50.0,45415,75068,82129,4.570854e+00,5.379279e+00,5.659200e+00,1,1,1, -Dox 100.0,52009,79365,87965,4.677907e+00,5.361092e+00,5.669696e+00,1,1,1, -Dox 200.0,63959,86725,96095,4.832942e+00,5.318321e+00,5.663546e+00,1,1,1, -Dox 500.0,80055,93869,107840,5.031924e+00,5.238768e+00,5.749740e+00,1,1,1, -Dox 1000.0,92173,95703,112858,5.198495e+00,5.184191e+00,5.822585e+00,1,1,1, -Dox 2000.0,102262,99465,119276,5.286472e+00,5.147556e+00,5.870413e+00,1,1,1, diff --git a/template_analysis/LacI-CAGop-batch.mat b/template_analysis/LacI-CAGop-batch.mat index e14a3bb..515999a 100644 Binary files a/template_analysis/LacI-CAGop-batch.mat and b/template_analysis/LacI-CAGop-batch.mat differ diff --git a/template_analysis/LacI-CAGop_histogramFile.csv b/template_analysis/LacI-CAGop_histogramFile.csv index 9196487..8002195 100644 --- a/template_analysis/LacI-CAGop_histogramFile.csv +++ b/template_analysis/LacI-CAGop_histogramFile.csv @@ -1,841 +1,841 @@ Id,BinCenters,BinCount_EYFP_MEFL,BinCount_mKate_MEFL,BinCount_EBFP2_MEFL -Dox 0.1,11220.1845430196,6806,2178,1373 -,14125.3754462276,8017,2753,2706 -,17782.7941003892,8782,3323,2637 -,22387.2113856834,8558,4640,2623 -,28183.8293126445,7617,4624,3739 -,35481.3389233575,6343,5595,4714 -,44668.3592150964,3931,5937,5304 -,56234.1325190349,1817,6282,5434 -,70794.5784384137,511,5747,5801 -,89125.0938133746,124,4272,4683 -,112201.845430196,21,3097,4012 -,141253.754462276,4,2284,3469 -,177827.941003892,4,2340,2917 -,223872.113856834,2,2545,3200 -,281838.293126445,2,2845,3612 -,354813.389233575,1,3390,3985 -,446683.592150963,2,3755,4034 -,562341.325190349,1,4031,3985 -,707945.784384137,0,4246,4135 -,891250.938133746,0,4436,4179 -,1122018.45430196,0,4502,4199 -,1412537.54462276,0,4289,4095 -,1778279.41003892,0,4007,3890 -,2238721.13856834,0,3630,3817 -,2818382.93126445,0,3244,3685 -,3548133.89233575,0,2738,3509 -,4466835.92150963,0,2203,3248 -,5623413.25190349,0,1731,3032 -,7079457.84384139,0,1406,2598 -,8912509.38133746,0,989,2401 -,11220184.5430196,0,769,1920 -,14125375.4462275,0,493,1626 -,17782794.1003892,0,391,1353 -,22387211.3856834,0,214,995 -,28183829.3126445,0,150,808 -,35481338.9233575,0,101,634 -,44668359.2150963,0,59,428 -,56234132.5190349,0,39,272 -,70794578.4384137,0,16,176 -,89125093.8133746,0,10,122 -,112201845.430197,0,1,86 -,141253754.462275,0,1,50 -,177827941.003892,0,0,30 -,223872113.856835,0,0,12 -,281838293.126445,0,0,4 -,354813389.233576,0,0,1 -,446683592.150962,0,0,1 -,562341325.190349,0,0,0 -,707945784.38414,0,0,0 -,891250938.133744,0,0,0 -,1122018454.30197,0,0,0 -,1412537544.62275,0,0,0 -,1778279410.03892,0,0,0 -,2238721138.56835,0,0,0 -,2818382931.26445,0,0,0 -,3548133892.33576,0,0,0 -,4466835921.50962,0,0,0 -,5623413251.90349,0,0,0 -,7079457843.8414,0,0,0 -,8912509381.33744,0,0,0 -Dox 0.2,11220.1845430196,5411,1798,1117 -,14125.3754462276,6643,2321,2113 -,17782.7941003892,7232,2718,2204 -,22387.2113856834,6995,3843,2132 -,28183.8293126445,6211,3862,3058 -,35481.3389233575,5331,4647,3846 -,44668.3592150964,3064,4891,4421 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+,1778000,2322,1949,4234 +,2239000,1876,1484,4167 +,2818000,1439,1113,3959 +,3548000,1041,835,4068 +,4467000,782,601,3804 +,5623000,543,447,3564 +,7079000,369,268,3371 +,8913000,255,201,3038 +,11220000,223,130,2646 +,14130000,112,91,2332 +,17780000,66,52,1857 +,22390000,42,34,1559 +,28180000,13,19,1240 +,35480000,9,11,926 +,44670000,6,6,760 +,56230000,0,3,486 +,70790000,1,1,344 +,89130000,0,1,248 +,112200000,0,0,164 +,141300000,0,0,87 +,177800000,0,0,66 +,223900000,0,0,42 +,281800000,0,0,12 +,354800000,0,0,2 +,446700000,0,0,0 +,562300000,0,0,0 +,707900000,0,0,0 +,891300000,0,0,0 +,1122000000,0,0,0 +,1413000000,0,0,0 +,1778000000,0,0,0 +,2239000000,0,0,0 +,2818000000,0,0,0 +,3548000000,0,0,0 +,4467000000,0,0,0 +,5623000000,0,0,0 +,7079000000,0,0,0 +,8913000000,0,0,0 +Dox 2000.0,11220,3157,2135,884 +,14130,3946,2510,1695 +,17780,4598,3211,1599 +,22390,4704,4287,1763 +,28180,4753,4561,2526 +,35480,4851,5423,3184 +,44670,3991,6146,3638 +,56230,3107,6735,3921 +,70790,2779,6380,4264 +,89130,2736,5502,3724 +,112200,2952,4725,3457 +,141300,3243,4165,3201 +,177800,3815,4164,2731 +,223900,4191,4160,2926 +,281800,4728,4333,3206 +,354800,4951,4426,3604 +,446700,5329,4311,3852 +,562300,5216,4280,3954 +,707900,5126,3867,4354 +,891300,4621,3343,4339 +,1122000,4322,2856,4472 +,1413000,3775,2144,4427 +,1778000,2983,1768,4663 +,2239000,2420,1330,4603 +,2818000,1772,935,4566 +,3548000,1345,640,4366 +,4467000,1029,475,4138 +,5623000,682,340,3914 +,7079000,527,217,3750 +,8913000,318,119,3303 +,11220000,208,88,3050 +,14130000,112,47,2539 +,17780000,73,26,2178 +,22390000,43,17,1768 +,28180000,20,7,1518 +,35480000,7,7,1085 +,44670000,3,4,764 +,56230000,2,1,521 +,70790000,0,0,381 +,89130000,0,0,225 +,112200000,0,0,147 +,141300000,0,0,106 +,177800000,0,0,58 +,223900000,0,0,28 +,281800000,0,0,20 +,354800000,0,0,9 +,446700000,0,0,2 +,562300000,0,0,1 +,707900000,0,0,0 +,891300000,0,0,0 +,1122000000,0,0,0 +,1413000000,0,0,0 +,1778000000,0,0,0 +,2239000000,0,0,0 +,2818000000,0,0,0 +,3548000000,0,0,0 +,4467000000,0,0,0 +,5623000000,0,0,0 +,7079000000,0,0,0 +,8913000000,0,0,0 diff --git a/template_analysis/LacI-CAGop_statisticsFile.csv b/template_analysis/LacI-CAGop_statisticsFile.csv index 5360a65..fedb858 100644 --- a/template_analysis/LacI-CAGop_statisticsFile.csv +++ b/template_analysis/LacI-CAGop_statisticsFile.csv @@ -1,15 +1,15 @@ -Id,BinCount_EYFP_MEFL,BinCount_mKate_MEFL,BinCount_EBFP2_MEFL,GeoMean_EYFP_MEFL,GeoMean_mKate_MEFL,GeoMean_EBFP2_MEFL,GeoStdDev_EYFP_MEFL,GeoStdDev_mKate_MEFL,GeoStdDev_EBFP2_MEFL -Dox 0.1,52543,109303,119534,22166.3892127889,249505.506639999,411999.810945553,1.60084886418747,6.76458209037627,8.11197502902936 -Dox 0.2,42961,88780,96134,22197.3585165184,248829.70817965,409394.898134347,1.5995070299618,6.86183513588093,8.13315768191834 -Dox 0.5,41068,85629,93335,22115.1197730026,257612.933359406,427307.331165168,1.59855221637465,6.86703936713332,8.13649642809853 -Dox 1.0,35885,75014,81850,22051.6025368397,258759.473832509,434883.202135694,1.60343323201745,6.91515508495032,8.22562195437244 -Dox 2.0,40232,83870,92116,22157.0039944486,250987.355176404,432747.679233904,1.60382703945833,6.75567397806102,8.1161867549061 -Dox 5.0,47577,98169,108567,22546.6135362971,248794.832186403,429718.109247681,1.64276006827997,6.8028174325622,8.28125154154586 -Dox 10.0,45162,92315,101005,22816.101591211,254771.721342507,427711.99314504,1.70266995382062,6.75700767951142,8.1256863136358 -Dox 20.0,49316,95836,105151,25395.162349766,257224.545603477,442090.53529095,1.99180114843258,6.76888717898788,8.30694414618095 -Dox 50.0,45606,75244,82319,37917.3791053317,242181.479602933,463724.365537185,3.0573604948584,6.45752985767407,8.41842393115125 -Dox 100.0,52347,79642,88193,48930.3361458285,232755.190533719,474127.864142354,3.68843886902498,6.16925999118782,8.43004507832824 -Dox 200.0,64190,86947,96290,69261.8115521469,210676.507867137,467542.79950384,4.50779976930361,5.86799325713468,8.25341761300255 -Dox 500.0,80463,94229,108153,109356.802892914,175204.602854373,570194.401672882,5.2828897137624,5.27822277454789,8.75049608606087 -Dox 1000.0,92324,95925,113074,159145.647766921,154514.40938562,673960.347664984,5.60321229394227,4.70603829679273,8.59943577186356 -Dox 2000.0,102447,99697,119441,194826.405465652,141750.506571001,749269.588700572,5.57840977677493,4.39004014516118,8.44799549981408 +Id,BinCount_EBFP2_MEFL,BinCount_EYFP_MEFL,BinCount_mKate_MEFL,GeoMean_EBFP2_MEFL,GeoMean_EYFP_MEFL,GeoMean_mKate_MEFL,GeoStdDev_EBFP2_MEFL,GeoStdDev_EYFP_MEFL,GeoStdDev_mKate_MEFL,GMM_Component1_Mean_EBFP2_MEFL,GMM_Component2_Mean_EBFP2_MEFL,GMM_Component1_Mean_EYFP_MEFL,GMM_Component2_Mean_EYFP_MEFL,GMM_Component1_Mean_mKate_MEFL,GMM_Component2_Mean_mKate_MEFL,GMM_Component1_Std_EBFP2_MEFL,GMM_Component2_Std_EBFP2_MEFL,GMM_Component1_Std_EYFP_MEFL,GMM_Component2_Std_EYFP_MEFL,GMM_Component1_Std_mKate_MEFL,GMM_Component2_Std_mKate_MEFL,GMM_Component1_Weight_EBFP2_MEFL,GMM_Component2_Weight_EBFP2_MEFL,GMM_Component1_Weight_EYFP_MEFL,GMM_Component2_Weight_EYFP_MEFL,GMM_Component1_Weight_mKate_MEFL,GMM_Component2_Weight_mKate_MEFL +Dox 0.1,52541,109291,119524,22170,249500,412000,1.601,6.765,8.112,17947.3362683252,17947.3362683252,41686.9383470336,981747.943019984,48083.9348449729,1210598.13355048,1.17262729784008,1.17262729784008,1.19756749597011,2.04691590227046,1.23029709912384,3.27642325685378,0.5,0.5,0.4195,0.5805,0.3215,0.6785 +Dox 0.2,42957,88776,96130,22200,248800,409400,1.6,6.862,8.133,17988.7091512879,17988.7091512879,41304.7501990161,1009252.88607668,47424.1985260245,1213388.85046498,1.17192548866257,1.17192548866257,1.19486819160792,2.04173794466953,1.22106842167489,3.25536732471636,0.5,0.5,0.4235,0.5765,0.3223,0.6777 +Dox 0.5,41068,85627,93331,22120,257600,427300,1.599,6.867,8.136,17906.0585403529,17906.0585403529,41209.751909733,1004615.79027839,48083.9348449729,1227439.23115841,1.17187152074203,1.17187152074203,1.19751234721868,2.06157908695264,1.23018378979159,3.28851630875983,0.5,0.5,0.4122,0.5878,0.3132,0.6868 +Dox 1.0,35884,75012,81845,22050,258800,434900,1.603,6.915,8.226,17864.8757485205,17864.8757485205,41399.967481973,1023292.99228075,47533.5225942805,1256029.96369488,1.17135894943295,1.17135894943295,1.19698856072794,2.0549440413453,1.22520849688522,3.2839761925048,0.5,0.5,0.4136,0.5864,0.3101,0.6899 +Dox 2.0,40228,83867,92109,22160,251000,432800,1.604,6.756,8.116,17906.0585403529,17906.0585403529,41686.9383470336,986279.48563121,47424.1985260245,1224616.19926505,1.1735997275116,1.1735997275116,1.19536352567372,2.02768271952128,1.22639395167575,3.26136945940879,0.5,0.5,0.4181,0.5819,0.3074,0.6926 +Dox 5.0,47572,98159,108552,22550,248800,429800,1.643,6.803,8.281,18113.400926196,265460.556197554,41304.7501990161,988553.094656939,47206.3041263591,1264736.34747115,1.17839258212882,1.23754215089203,1.19690587854322,2.03798038628706,1.22224987072109,3.29609712177458,0.9979,0.00208,0.4196,0.5804,0.3155,0.6845 +Dox 10.0,45160,92309,101004,22820,254800,427700,1.703,6.757,8.126,18030.1774085957,180717.412601093,41495.4042634363,984011.105761135,47097.7326396953,1210598.13355048,1.18053807877441,1.38995263121335,1.19798119256848,2.02208775840144,1.2184283627084,3.28624546658205,0.992,0.008019,0.4119,0.5881,0.3083,0.6917 +Dox 20.0,49313,95832,105147,25400,257200,442100,1.992,6.769,8.307,18365.3834334835,98401.1105761135,41304.7501990161,1009252.88607668,47206.3041263591,1267651.86585784,1.18907705818097,1.77827941003892,1.19577646091624,1.97287695552572,1.21590599570883,3.35274095848416,0.9397,0.06033,0.4139,0.5861,0.3078,0.6922 +Dox 50.0,45595,75231,82305,37920,242200,463800,3.058,6.458,8.418,18578.044550917,136458.313658892,41304.7501990161,918332.596483581,46881.3382145266,1273503.08101666,1.191516333218,1.97015320721676,1.19583152972531,1.92043671394335,1.22042192167403,3.50267626913813,0.7629,0.2371,0.4158,0.5842,0.2938,0.7062 +Dox 100.0,52342,79636,88188,48930,232800,474200,3.689,6.17,8.43,18923.4361864498,172583.78919902,40926.0659730011,822242.649947071,47643.0986805416,1327394.45772974,1.19704368535755,2.05968117659736,1.19555621103835,1.90985325856624,1.22698710912328,3.42136966135368,0.6792,0.3208,0.4067,0.5933,0.2981,0.7019 +Dox 200.0,64182,86937,96281,69270,210700,467500,4.508,5.868,8.254,19275.2491319094,230144.181740851,41783.0366646622,732824.533138904,48528.8500162121,1306170.88813184,1.19718150803838,2.182729911843,1.19715394223281,1.92043671394335,1.23128900107556,3.30597831070432,0.5791,0.4209,0.4201,0.5799,0.3001,0.6999 +Dox 500.0,80451,94217,108139,109400,175200,570300,5.283,5.278,8.75,19543.394557754,316227.766016838,40271.7034325459,539510.622515128,49203.9535681451,1566751.07010815,1.20143422654464,2.17070096839771,1.19088547969925,1.9350847929379,1.22992888194808,3.42373387626452,0.4608,0.5392,0.4174,0.5826,0.281,0.719 +Dox 1000.0,92313,95917,113064,159200,154500,674000,5.603,4.706,8.599,20464.4463672467,407380.277804113,40550.8535448383,402717.03432546,53210.8259266794,1725837.8919902,1.21149046392586,2.08593129583112,1.19302625137364,1.92486377778253,1.25765059321642,3.33733651305149,0.3769,0.6231,0.4017,0.5983,0.2601,0.7399 +Dox 2000.0,102435,99685,119424,194800,141700,749400,5.579,4.39,8.448,22029.2646305346,485288.500162121,42169.6503428582,363915.036127207,54701.5962893972,1828100.21614274,1.23148747740937,1.91646106273539,1.20331685511764,1.84119590368765,1.26911214444519,3.2351915531421,0.3486,0.6514,0.4211,0.5789,0.2456,0.7544 diff --git a/template_analysis/batch_template.m b/template_analysis/batch_template.m index 9d48604..7b9060f 100644 --- a/template_analysis/batch_template.m +++ b/template_analysis/batch_template.m @@ -30,26 +30,26 @@ % Make a map of condition names to file sets stem1011 = '../example_assay/LacI-CAGop_'; file_pairs = {... - 'Dox 0.1', {[stem1011 'B3_B03_P3.fcs']}; % Replicates go here, e.g., {[rep1], [rep2], [rep3]} - 'Dox 0.2', {[stem1011 'B4_B04_P3.fcs']}; - 'Dox 0.5', {[stem1011 'B5_B05_P3.fcs']}; - 'Dox 1.0', {[stem1011 'B6_B06_P3.fcs']}; - 'Dox 2.0', {[stem1011 'B7_B07_P3.fcs']}; - 'Dox 5.0', {[stem1011 'B8_B08_P3.fcs']}; - 'Dox 10.0', {[stem1011 'B9_B09_P3.fcs']}; - 'Dox 20.0', {[stem1011 'B10_B10_P3.fcs']}; - 'Dox 50.0', {[stem1011 'B11_B11_P3.fcs']}; - 'Dox 100.0', {[stem1011 'B12_B12_P3.fcs']}; - 'Dox 200.0', {[stem1011 'C1_C01_P3.fcs']}; - 'Dox 500.0', {[stem1011 'C2_C02_P3.fcs']}; - 'Dox 1000.0', {[stem1011 'C3_C03_P3.fcs']}; - 'Dox 2000.0', {[stem1011 'C4_C04_P3.fcs']}; + 'Dox 0.1', {[stem1011 'B3_P3.fcs']}; % Replicates go here, e.g., {[rep1], [rep2], [rep3]} + 'Dox 0.2', {[stem1011 'B4_P3.fcs']}; + 'Dox 0.5', {[stem1011 'B5_P3.fcs']}; + 'Dox 1.0', {[stem1011 'B6_P3.fcs']}; + 'Dox 2.0', {[stem1011 'B7_P3.fcs']}; + 'Dox 5.0', {[stem1011 'B8_P3.fcs']}; + 'Dox 10.0', {[stem1011 'B9_P3.fcs']}; + 'Dox 20.0', {[stem1011 'B10_P3.fcs']}; + 'Dox 50.0', {[stem1011 'B11_P3.fcs']}; + 'Dox 100.0', {[stem1011 'B12_P3.fcs']}; + 'Dox 200.0', {[stem1011 'C1_P3.fcs']}; + 'Dox 500.0', {[stem1011 'C2_P3.fcs']}; + 'Dox 1000.0', {[stem1011 'C3_P3.fcs']}; + 'Dox 2000.0', {[stem1011 'C4_P3.fcs']}; }; n_conditions = size(file_pairs,1); % Execute the actual analysis -[results sampleresults] = per_color_constitutive_analysis(CM,file_pairs,{'EBFP2','EYFP','mKate'},AP); +[results, sampleresults] = per_color_constitutive_analysis(CM,file_pairs,{'EYFP','mKate', 'EBFP2'},AP); % Make output plots TASBEConfig.set('OutputSettings.StemName','LacI-CAGop'); diff --git a/template_analysis/plusminus_template.m b/template_analysis/plusminus_template.m index fe9cb6b..3d4bd1b 100755 --- a/template_analysis/plusminus_template.m +++ b/template_analysis/plusminus_template.m @@ -35,18 +35,17 @@ batch_description = {... {'Lows';'BaseDox';{'+', '-', 'control'}; % First set is the matching "plus" conditions - {0.1, {[stem1011 'C3_C03_P3.fcs']}; % Replicates go here, e.g., {[rep1], [rep2], [rep3]} - 0.2, {[stem1011 'C4_C04_P3.fcs']}}; - % Second set is the matching "minus" conditions - {0.1, {[stem1011 'B3_B03_P3.fcs']}; - 0.2, {[stem1011 'B4_B04_P3.fcs']}}; - {0.1, {[stem1011 'B9_B09_P3.fcs']}; % Replicates go here, e.g., {[rep1], [rep2], [rep3]} - 0.2, {[stem1011 'B10_B10_P3.fcs']}}}; + {0.1, {[stem1011 'C3_P3.fcs']}; % Replicates go here, e.g., {[rep1], [rep2], [rep3]} + 0.2, {[stem1011 'C4_P3.fcs']}}; + {0.1, {[stem1011 'B3_P3.fcs']}; + 0.2, {[stem1011 'B4_P3.fcs']}}; + {0.1, {[stem1011 'B9_P3.fcs']}; + 0.2, {[stem1011 'B10_P3.fcs']}}}; {'Highs';'BaseDox';{'+', '-'}; - {10, {[stem1011 'C3_C03_P3.fcs']}; - 20, {[stem1011 'C4_C04_P3.fcs']}}; - {10, {[stem1011 'B9_B09_P3.fcs']}; - 20, {[stem1011 'B10_B10_P3.fcs']}}}; + {10, {[stem1011 'C3_P3.fcs']}; + 20, {[stem1011 'C4_P3.fcs']}}; + {10, {[stem1011 'B9_P3.fcs']}; + 20, {[stem1011 'B10_P3.fcs']}}}; }; % Execute the actual analysis diff --git a/template_analysis/transfercurve_template.m b/template_analysis/transfercurve_template.m index 3c2e42d..9137121 100644 --- a/template_analysis/transfercurve_template.m +++ b/template_analysis/transfercurve_template.m @@ -33,20 +33,20 @@ % Make a map of induction levels to file sets stem1011 = '../example_assay/LacI-CAGop_'; level_file_pairs = {... - 0.1, {[stem1011 'B3_B03_P3.fcs']}; % Replicates go here, e.g., {[rep1], [rep2], [rep3]} - 0.2, {[stem1011 'B4_B04_P3.fcs']}; - 0.5, {[stem1011 'B5_B05_P3.fcs']}; - 1.0, {[stem1011 'B6_B06_P3.fcs']}; - 2.0, {[stem1011 'B7_B07_P3.fcs']}; - 5.0, {[stem1011 'B8_B08_P3.fcs']}; - 10.0, {[stem1011 'B9_B09_P3.fcs']}; - 20.0, {[stem1011 'B10_B10_P3.fcs']}; - 50.0, {[stem1011 'B11_B11_P3.fcs']}; - 100.0, {[stem1011 'B12_B12_P3.fcs']}; - 200.0, {[stem1011 'C1_C01_P3.fcs']}; - 500.0, {[stem1011 'C2_C02_P3.fcs']}; - 1000.0, {[stem1011 'C3_C03_P3.fcs']}; - 2000.0, {[stem1011 'C4_C04_P3.fcs']}; + 0.1, {[stem1011 'B3_P3.fcs']}; % Replicates go here, e.g., {[rep1], [rep2], [rep3]} + 0.2, {[stem1011 'B4_P3.fcs']}; + 0.5, {[stem1011 'B5_P3.fcs']}; + 1.0, {[stem1011 'B6_P3.fcs']}; + 2.0, {[stem1011 'B7_P3.fcs']}; + 5.0, {[stem1011 'B8_P3.fcs']}; + 10.0, {[stem1011 'B9_P3.fcs']}; + 20.0, {[stem1011 'B10_P3.fcs']}; + 50.0, {[stem1011 'B11_P3.fcs']}; + 100.0, {[stem1011 'B12_P3.fcs']}; + 200.0, {[stem1011 'C1_P3.fcs']}; + 500.0, {[stem1011 'C2_P3.fcs']}; + 1000.0, {[stem1011 'C3_P3.fcs']}; + 2000.0, {[stem1011 'C4_P3.fcs']}; }; experiment = Experiment(experimentName,{inducer_name}, level_file_pairs); @@ -59,8 +59,8 @@ % Plot how the constitutive fluorescence was distributed TASBEConfig.set('OutputSettings.DeviceName',device_name); -TASBEConfig.set('histogram.displayLegend',false); -plot_bin_statistics(sampleresults); +% TASBEConfig.set('histogram.displayLegend',false); +plot_bin_statistics(sampleresults, getInducerLevelsToFiles(experiment,1)); % Plot the relation between inducer and input fluorescence TASBEConfig.set('OutputSettings.DeviceName',inducer_name); diff --git a/template_colormodel/CM120312.mat b/template_colormodel/CM120312.mat index 81fe5cf..414f0fb 100644 Binary files a/template_colormodel/CM120312.mat and b/template_colormodel/CM120312.mat differ