dendrogram is basically a group of lines. Thus, you will have to change the color of each lines accordingly -
load fisheriris
%orgcolor = colororder('default'); % 配色の決定(この配色をクラスターに使用)
Z = linkage(meas,'average','chebychev'); % 階層クラスターツリーの作成
cutoff = median([Z(end-2,3) Z(end-1,3)]); % クラスターを3つに分けれるよう中間点でカット
%% Original Figure
figure
dendrogram(Z,'ColorThreshold',cutoff); % 系統樹を作成
%% Modified Figure
figure
d = dendrogram(Z,'ColorThreshold',cutoff); % 系統樹を作成
Col = vertcat(d.Color);
[or, ~, idx] = unique(Col, 'rows')
%define new colors
newcolors = hsv(4)
%Change the corresponding colors
for k = 1:size(or, 1)
arr = idx==k;
set(d(arr), 'Color', newcolors(k, :))
end
