MATLAB: How to create a heat map without the dendrogram

heatmapMATLABno

I would like to create a heat map that does not include a dendrogram. The MATLAB function CLUSTERGRAM creates a dendrogram and a heat map but it does not have the option of creating only a heat map.

Best Answer

To create a heat map without a dendrogram use the IMAGESC function as shown below:

data = gallery('invhess',20);
imagesc(data)
axis off

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MATLAB: How to create/find a bam index file for using the bamread function

You can use a BioMap object to load the information from the BAM file without the BAI file. See instructions here: http://www.mathworks.com/help/bioinfo/ug/storing-and-managing-short-read-sequence-data-in-objects.html

For example if you want to load the data from chromosome 1, you do this:

info = baminfo(bamFilename,'ScanDictionary',true);
bm = BioMap(bamFilename, 'SelectReference', 'ChrI');

Instead of 'ChrI' you can put any of the references that were used for mapping. These are stored here:

info.ScannedDictionary

The BioMap line will also generate a BAI file which you can use in bamread but that usually takes a lot more memory and it is slower.

MATLAB: How to extract a colormap from a dendrogram

Hello Rebecca,

I have a brute force solution for a few clusters. It looks like 'dendrogram' use the hsv colormap, and clusters with only 1 member are set to be black. The rest of the clusters are colored from

So what you can do is:

% Clustering
nClus = 10;                                         % Let's say you have 10 clusters
clustTreeEuc = linkage(eucD,'average');             % By average euclidean distance
color = clustTreeEuc(end-nClus+2,3)-eps;            % Calc. threshold based on nClus
[H,T,perm] = dendrogram(clustTreeEuc,0,'Orientation','right','ColorThreshold',...
    color,'labels','myDataNames');                  % Plot dendrogram
hidx = cluster(clustTreeEuc,'criterion','distance',...
    'MaxClust',nClus);                            % idx of data in each clus
% After you plot the dendrogram, find out what color each cluster is
% You can use histcounts(hidx) to help you
% By the order of the rainbow (r y g b ...) assign each cluster a new number
% For e.g. clus 1 is green, new no. is 3. Clus 2 is red, new no. is 1 etc.
% Black is the last color (clusters with 1 member)
cidx = [4 1 7 3 8 2 6 5 9 9];   % Example with two 1 member clusters (so 9 colors)
% Colors
cmap = hsv(max(cidx)-1);
cmap(end+1,:) = [0 0 0];
cmap(cidx(hidx(i)),:)       % This gives color of ith data

Hope it helps! If anyone finds a better method please let me know, thanks!

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Related Solutions

MATLAB: How to create/find a bam index file for using the bamread function

MATLAB: How to extract a colormap from a dendrogram

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