finished adjusting for issue 429

Author: jakebeal

03_flow_MEFL/exercises.m

@@ -87,7 +87,7 @@
 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 +152,7 @@
 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

@@ -58,8 +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
@@ -74,7 +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