Merge pull request #66 from TASBE/fix/issue.429

Update to match fix of issue.429

Author: jakebeal

02_flow_compensation/exercises.m

@@ -103,8 +103,6 @@
 
 colorpairfiles = {};
 CM = ColorModel(beadfile, blankfile, channels, colorfiles, colorpairfiles);
-CM=set_translation_plot(CM, true);
-CM=set_noise_plot(CM, true);
 
 TASBEConfig.set('beads.beadModel','SpheroTech RCP-30-5A'); % Entry from BeadCatalog.xls matching your beads
 TASBEConfig.set('beads.beadBatch','Lot AA01, AA02, AA03, AA04, AB01, AB02, AC01, GAA01-R'); % Entry from BeadCatalog.xls containing your lot

03_flow_MEFL/exercises.m

@@ -72,8 +72,6 @@
 colorpairfiles{2} = {channels{2}, channels{3}, channels{1}, [colordata '2012-03-12_mkate_EBFP2_EYFP_P3.fcs']};
 colorpairfiles{3} = {channels{2}, channels{1}, channels{3}, [colordata '2012-03-12_mkate_EBFP2_EYFP_P3.fcs']};
 CM = ColorModel(beadfile, blankfile, channels, colorfiles, colorpairfiles);
-CM=set_translation_plot(CM, true);
-CM=set_noise_plot(CM, true);
 
 TASBEConfig.set('beads.beadModel','SpheroTech RCP-30-5A'); % Entry from BeadCatalog.xls matching your beads
 TASBEConfig.set('beads.beadBatch','Lot AA01, AA02, AA03, AA04, AB01, AB02, AC01, GAA01-R'); % Entry from BeadCatalog.xls containing your lot
@@ -86,8 +84,7 @@
 CM=set_dequantization(CM, 1); % important at low levels
 TASBEConfig.set('beads.rangeMin', 1); % Don't consider beads less than this 10^1 amount
 % Things we'll talk about in the next section...
-CM=set_translation_plot(CM, true); 
-CM=set_translation_channel_min(CM,[2,2,2]);
+TASBEConfig.set('colortranslation.channelMinimum',[2,2,2]);
 % and build it!
 CM = resolve(CM); % plots1
 
@@ -152,7 +149,7 @@
 fcs_scatter(DataFile('fcs', [colordata '2012-03-12_mkate_EBFP2_EYFP_P3.fcs']),'FITC-A','Pacific Blue-A',0,[0 0; 6 6],1); % Fig6
 % Notice that it's only nicely linear for the higher levels, 
 % and that it's much smearier than our compensation controls
-% The first is what set_translation_channel_min is for
+% The first is what setting colortranslation.channelMinimum is for
 
 % The way we partition is controlled by the colorpairfiles configuration:
 % colorpairfiles{1} = {channels{1}, channels{3}, channels{2}, [colordata '2012-03-12_mkate_EBFP2_EYFP_P3.fcs']};

template_colormodel/make_color_model.m

@@ -7,16 +7,14 @@
 blankfile = DataFile('fcs', [stem0312 'blank_P3.fcs']);
 
 % Autodetect gating with an N-dimensional gaussian-mixture-model
-AGP = AutogateParameters();
-% Adjust AGP values if needed.  The most common adjustments are below:
-% These are the most common values to adjust:
-% Match t
-%AGP.channel_names = {'FSC-A','SSC-A','FSC-H','FSC-W','SSC-H','SSC-W'};
+% Adjust gating values if needed.  The most common adjustments are below:
+% Channels to be used:
+%TASBEConfig.set('gating.channelNames') = {'FSC-A','SSC-A','FSC-H','FSC-W','SSC-H','SSC-W'};
 % Typically two components: one tight single-cell component, one diffuse 
 % non-cell or clump component.  More complex distributions may need more.
-%AGP.k_components = 2;
-%AGP.selected_components = [1];
-autogate = GMMGating(blankfile,AGP,'plots');
+%TASBEConfig.set('gating.kComponents') = 2;
+%TASBEConfig.set('selectedComponents') = [1];
+autogate = GMMGating(blankfile);
 
 % Create one channel / colorfile pair for each color
 channels = {}; colorfiles = {};
@@ -60,8 +58,6 @@
 % sizebeadfile = '../example_controls/180614_PPS6K_A02.fcs';
 
 CM = ColorModel(beadfile, blankfile, channels, colorfiles, colorpairfiles, sizebeadfile);
-CM=set_translation_plot(CM, true);
-CM=set_noise_plot(CM, true);
 
 TASBEConfig.set('beads.beadModel','SpheroTech RCP-30-5A'); % Entry from BeadCatalog.xls matching your beads
 TASBEConfig.set('beads.beadBatch','Lot AA01, AA02, AA03, AA04, AB01, AB02, AC01, GAA01-R'); % Entry from BeadCatalog.xls containing your lot
@@ -76,7 +72,7 @@
 %TASBEConfig.set('beads.peakThreshold', 200);
 CM=set_ERF_channel_name(CM, 'FITC-A');
 % Ignore channel data for ith channel if below 10^[value(i)]
-CM=set_translation_channel_min(CM,[2,2,2]);
+TASBEConfig.set('colortranslation.channelMinimum',[2,2,2]);
 
 % Configuration for size beads, if used
 % TASBEConfig.set('sizebeads.beadModel','SpheroTech PPS-6K'); % Entry from BeadCatalog.xls matching your beads