Skip to content

Commit

Permalink
Adding sampling to bead removal step.
Browse files Browse the repository at this point in the history
  • Loading branch information
@rfinck
rfinck committed Jul 31, 2014
1 parent 87575b7 commit ce59021
Show file tree
Hide file tree
Showing 2 changed files with 45 additions and 35 deletions.
75 changes: 41 additions & 34 deletions norm_cytof.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -422,20 +422,33 @@ function change_figpos(src,event)
global figpos
global num_beads

tdata=asinh(1/5*obj.data(:,obj.bead_channels));
tdata=asinh(1/5*obj.data(:,obj.bead_channels));

if sum(obj.beads)>num_beads
mdists=mahal(tdata,tdata(obj.beads,:));
mdists=sqrt(mdists);
mdists=mahal(tdata,tdata(obj.beads,:));
mdists=sqrt(mdists);

%sample for visualization if too many cells
num_cells=size(tdata,1);
if num_cells>100000
inds=randsample(num_cells,100000);
tdata_sampled=tdata(inds,:);
mdists_sampled=mdists(inds,:);
else
tdata_sampled=tdata;
mdists_sampled=mdists;
end
else
% obj.removed_events=[obj.data(~notbeads,:) mdists(~notbeads)];
obj.data=[obj.data zeros(size(obj.data,1),1)];
obj.channelnames=[obj.channelnames 'beadDist'];
obj.markernames=[obj.markernames 'beadDist'];
obj.mahal_cutoff=0;
h=warndlg(['Too few beads to estimate distances in ' obj.header.filename ': you must remove them manually.'] ,'Sparse beads!');
waitfor(h)
drawnow
return

% obj.removed_events=[obj.data(~notbeads,:) mdists(~notbeads)];
obj.data=[obj.data zeros(size(obj.data,1),1)];
obj.channelnames=[obj.channelnames 'beadDist'];
obj.markernames=[obj.markernames 'beadDist'];
obj.mahal_cutoff=0;
h=warndlg(['Too few beads to estimate distances in ' obj.header.filename ': you must remove them manually.'] ,'Sparse beads!');
waitfor(h)
drawnow
return
end


Expand All @@ -448,8 +461,8 @@ function change_figpos(src,event)
% fig=figure('position',[1 0.3*sc(4) sc(3) sc(3)/3]);

nbins=20;
[~,bin]=histc(mdists,0:nbins);

[~,bin]=histc(mdists_sampled,0:nbins);
cm=flipud(jet(nbins+1));
colormap(cm);
obj.numcm=nbins+1;
Expand All @@ -462,32 +475,32 @@ function change_figpos(src,event)
ax=zeros(1,3);
ax(1)=axes('position',[0.0625 0.1 0.25 0.75]);
hold on
plot(tdata(bin==0,combos(1,1)),tdata(bin==0,combos(1,2)),'+','color',cm(end,:),'markersize',2)
plot(tdata_sampled(bin==0,combos(1,1)),tdata_sampled(bin==0,combos(1,2)),'+','color',cm(end,:),'markersize',2)
for j=1:nbins
i=nbins+1-j;
plot(tdata(bin==i,combos(1,1)),tdata(bin==i,combos(1,2)),'+','color',cm(i,:),'markersize',2)
plot(tdata_sampled(bin==i,combos(1,1)),tdata_sampled(bin==i,combos(1,2)),'+','color',cm(i,:),'markersize',2)
end

xlabel(obj.channelnames{obj.bead_channels(combos(1,1))})
ylabel(obj.channelnames{obj.bead_channels(combos(1,2))})

ax(2)=axes('position',[0.375 0.1 0.25 0.75]);
hold on
plot(tdata(bin==0,combos(end-1,1)),tdata(bin==0,combos(end-1,2)),'+','color',cm(end,:),'markersize',2)
plot(tdata_sampled(bin==0,combos(end-1,1)),tdata_sampled(bin==0,combos(end-1,2)),'+','color',cm(end,:),'markersize',2)
for j=1:nbins
i=nbins+1-j;
plot(tdata(bin==i,combos(end-1,1)),tdata(bin==i,combos(end-1,2)),'+','color',cm(i,:),'markersize',2)
plot(tdata_sampled(bin==i,combos(end-1,1)),tdata_sampled(bin==i,combos(end-1,2)),'+','color',cm(i,:),'markersize',2)
end

xlabel(obj.channelnames{obj.bead_channels(combos(end-1,1))})
ylabel(obj.channelnames{obj.bead_channels(combos(end-1,2))})

ax(3)=axes('position',[0.6875 0.1 0.25 0.75]);
hold on
plot(tdata(bin==0,combos(end,1)),tdata(bin==0,combos(end,2)),'+','color',cm(end,:),'markersize',2)
plot(tdata_sampled(bin==0,combos(end,1)),tdata_sampled(bin==0,combos(end,2)),'+','color',cm(end,:),'markersize',2)
for j=1:nbins
i=nbins+1-j;
plot(tdata(bin==i,combos(end,1)),tdata(bin==i,combos(end,2)),'+','color',cm(i,:),'markersize',2)
plot(tdata_sampled(bin==i,combos(end,1)),tdata_sampled(bin==i,combos(end,2)),'+','color',cm(i,:),'markersize',2)
end

xlabel(obj.channelnames{obj.bead_channels(combos(end,1))})
Expand All @@ -503,9 +516,9 @@ function change_figpos(src,event)
ax=axes('position',[0.375 0.1 0.25 0.75]);
hold on
for i=1:nbins
plot(tdata(bin==i,1),tdata(bin==i,2),'+','color',cm(i,:),'markersize',2)
plot(tdata_sampled(bin==i,1),tdata_sampled(bin==i,2),'+','color',cm(i,:),'markersize',2)
end
plot(tdata(bin==0,1),tdata(bin==0,2),'+','color',cm(end,:),'markersize',2)
plot(tdata_sampled(bin==0,1),tdata_sampled(bin==0,2),'+','color',cm(end,:),'markersize',2)
xlabel(obj.channelnames{obj.bead_channels(1)})
ylabel(obj.channelnames{obj.bead_channels(2)})

Expand Down Expand Up @@ -541,14 +554,14 @@ function change_figpos(src,event)
% else
QuestOpt.Position=questpos;
if nargin<3
defAns={''};
defAns={''};
end
while (1)
cutoff=str2double(myInputdlg({'Type in the cutoff, then press Enter. (You can enter 0 if you do not want to apply a cutoff.)'},...
'Choose Cutoff',1,defAns,QuestOpt));
if 0<=cutoff && cutoff<Inf && ~isnan(cutoff)
break
end
cutoff=str2double(myInputdlg({'Type in the cutoff, then press Enter. (You can enter 0 if you do not want to apply a cutoff.)'},...
'Choose Cutoff',1,defAns,QuestOpt));
if 0<=cutoff && cutoff<Inf && ~isnan(cutoff)
break
end
end


Expand All @@ -563,12 +576,6 @@ function change_figpos(src,event)
obj.markernames=[obj.markernames 'beadDist'];

obj.mahal_cutoff=cutoff;







function mahal_cutoff(src,event)
shift=false;
Expand Down
5 changes: 4 additions & 1 deletion normalize_folder.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -245,7 +245,10 @@ function normalize_folder(varargin)
if strcmp(quest,'Yes')
[oldBead_files,oldBead_dir] = uigetfile({'*.fcs','*.FCS'},'Choose File(s) of Gated Beads','MultiSelect','on');
if oldBead_dir==0
return
h=warndlg('No bead files selected! Normalizing to the median bead level.' ,'No files selected');
waitfor(h)
drawnow
bead_means=median(allbeads(:,2:(num_beads+1)));
else
if iscell(oldBead_files) %selected > 1 fcs file

Expand Down

0 comments on commit ce59021

Please sign in to comment.