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Flow Cytometry Data Reader and Visualization

version 1.1.0.1 (189 KB) by

Flow Cytometry Data Reader and Visualization Example

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Updated

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This includes a function to read in the standard flow cytometry FCS format data and examples of how to visualize the data.

Comments and Ratings (12)

yqf229118

very good,

Will the fcsread function work for fcs3.0 file type?

I get this error

Error using reshape
Size arguments must be real integers.

Error in fcsread (line 81)
textHeader = reshape(textCell,2,numel(textCell)/2)';

Chad Greene

Chad Greene (view profile)

The dscatter function is insanely fast and well written. It's beautifully documented and easy to use.

I used dscatter on a 1.5 million point dataset and the only bottleneck in processing is Matlab's scatter command. So I replaced the line of code which calls scatter and instead I'm using Aslak Grinsted's fastscatter, which is available on File Exchange. Here's what I replaced it with:

h = fastscatter(X,Y,col,'markersize',msize);

Now, dscatter takes 0.37 seconds to calculate and plot 1.5 million points. That's quite good.

The input parser wasn't detecting my request to set the marker size, so I added this to line 105:

tmp = strcmpi(varargin,'msize');
if any(tmp)
   msize = varargin{find(tmp)+1};
else
   msize = 10;
end

Thanks for writing and sharing this clever, efficient code, Robert!

I am getting an error, when using the dscatter function:
Error using histc
Edge vector must be monotonically non-decreasing

Any idea on what might be causing it?

Ruben

Ruben (view profile)

Raphael

The file return errors for input with NaN values (not necessary a bad thing).

F Poelwijk

F Poelwijk

arnold

arnold (view profile)

cool, but I cannot seem to set the marker size or non filled markers. Works fine with 'plot' mesh or grid, but not with 'msize:
==================================
>> h = dscatter(X, Y, 'msize', 20);
Error using scatter (line 53)
Too many input arguments.

Error in dscatter (line 170)
                h =
                scatter(X,Y,msize,col,marker,'filled');
==================================

It would also be nice if one could generate a gapless 2D image/array with the "density" as entries. Like the 2d projection of what ('plot', 'surf') actualy gives you.

On top of that I'd recommend catching the input "error" of horizontal vectors instead of vertical. It gives the user an error about equal sizes, you should just check for that and rotate the vectors if necessary ;)

Raz Shimoni

Sean Wang

Finally! I've been waiting for a long time

Updates

1.1.0.1

Updated license

1.1

Add BSD license

MATLAB Release
MATLAB 7.0.4 (R14SP2)
Acknowledgements

Inspired: Ratiometric FRET, FlowPlot, TACTICS Toolbox

Download apps, toolboxes, and other File Exchange content using Add-On Explorer in MATLAB.

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