Commit Friday evening.
PDFA and EXFO Laser are now part of the family
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Silas Labor Zizou
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function violins = violinplot(data, cats, varargin)
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%Violinplots plots violin plots of some data and categories
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% VIOLINPLOT(DATA) plots a violin of a double vector DATA
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%
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% VIOLINPLOT(DATAMATRIX) plots violins for each column in
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% DATAMATRIX.
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%
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% VIOLINPLOT(DATAMATRIX, CATEGORYNAMES) plots violins for each
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% column in DATAMATRIX and labels them according to the names in the
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% cell-of-strings CATEGORYNAMES.
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%
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% In the cases above DATA and DATAMATRIX can be a vector or a matrix,
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% respectively, either as is or wrapped in a cell.
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% To produce violins which have one distribution on one half and another
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% one on the other half, DATA and DATAMATRIX have to be cell arrays
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% with two elements, each containing a vector or a matrix. The number of
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% columns of the two data sets has to be the same.
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%
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% VIOLINPLOT(DATA, CATEGORIES) where double vector DATA and vector
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% CATEGORIES are of equal length; plots violins for each category in
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% DATA.
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%
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% VIOLINPLOT(TABLE), VIOLINPLOT(STRUCT), VIOLINPLOT(DATASET)
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% plots violins for each column in TABLE, each field in STRUCT, and
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% each variable in DATASET. The violins are labeled according to
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% the table/dataset variable name or the struct field name.
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%
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% violins = VIOLINPLOT(...) returns an object array of
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% <a href="matlab:help('Violin')">Violin</a> objects.
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%
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% VIOLINPLOT(..., 'PARAM1', val1, 'PARAM2', val2, ...)
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% specifies optional name/value pairs for all violins:
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% 'Width' Width of the violin in axis space.
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% Defaults to 0.3
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% 'Bandwidth' Bandwidth of the kernel density estimate.
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% Should be between 10% and 40% of the data range.
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% 'ViolinColor' Fill color of the violin area and data points. Accepts
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% 1x3 color vector or nx3 color vector where n = num
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% groups. In case of two data sets being compared it can
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% be an array of up to two cells containing nx3
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% matrices.
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% Defaults to the next default color cycle.
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% 'ViolinAlpha' Transparency of the violin area and data points.
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% Can be either a single scalar value or an array of
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% up to two cells containing scalar values.
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% Defaults to 0.3.
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% 'MarkerSize' Size of the data points, if shown.
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% Defaults to 24
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% 'MedianMarkerSize' Size of the median indicator, if shown.
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% Defaults to 36
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% 'EdgeColor' Color of the violin area outline.
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% Defaults to [0.5 0.5 0.5]
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% 'BoxColor' Color of the box, whiskers, and the outlines of
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% the median point and the notch indicators.
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% Defaults to [0.5 0.5 0.5]
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% 'MedianColor' Fill color of the median and notch indicators.
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% Defaults to [1 1 1]
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% 'ShowData' Whether to show data points.
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% Defaults to true
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% 'ShowNotches' Whether to show notch indicators.
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% Defaults to false
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% 'ShowMean' Whether to show mean indicator
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% Defaults to false
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% 'ShowBox' Whether to show the box.
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% Defaults to true
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% 'ShowMedian' Whether to show the median indicator.
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% Defaults to true
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% 'ShowWhiskers' Whether to show the whiskers
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% Defaults to true
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% 'GroupOrder' Cell of category names in order to be plotted.
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% Defaults to alphabetical ordering
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% Copyright (c) 2016, Bastian Bechtold
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% This code is released under the terms of the BSD 3-clause license
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hascategories = exist('cats','var') && not(isempty(cats));
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%parse the optional grouporder argument
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%if it exists parse the categories order
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% but also delete it from the arguments passed to Violin
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grouporder = {};
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idx=find(strcmp(varargin, 'GroupOrder'));
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if ~isempty(idx) && numel(varargin)>idx
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if iscell(varargin{idx+1})
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grouporder = varargin{idx+1};
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varargin(idx:idx+1)=[];
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else
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error('Second argument of ''GroupOrder'' optional arg must be a cell of category names')
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end
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end
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% check and correct the structure of ViolinColor input
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idx=find(strcmp(varargin, 'ViolinColor'));
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if ~isempty(idx) && iscell(varargin{idx+1})
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if length(varargin{idx+1}(:))>2
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error('ViolinColor input can be at most a two element cell array');
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end
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elseif ~isempty(idx) && isnumeric(varargin{idx+1})
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varargin{idx+1} = varargin(idx+1);
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end
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% check and correct the structure of ViolinAlpha input
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idx=find(strcmp(varargin, 'ViolinAlpha'));
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if ~isempty(idx) && iscell(varargin{idx+1})
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if length(varargin{idx+1}(:))>2
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error('ViolinAlpha input can be at most a two element cell array');
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end
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elseif ~isempty(idx) && isnumeric(varargin{idx+1})
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varargin{idx+1} = varargin(idx+1);
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end
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% tabular data
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if isa(data, 'dataset') || isstruct(data) || istable(data)
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if isa(data, 'dataset')
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colnames = data.Properties.VarNames;
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elseif istable(data)
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colnames = data.Properties.VariableNames;
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elseif isstruct(data)
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colnames = fieldnames(data);
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end
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catnames = {};
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if isempty(grouporder)
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for n=1:length(colnames)
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if isnumeric(data.(colnames{n}))
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catnames = [catnames colnames{n}]; %#ok<*AGROW>
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end
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end
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catnames = sort(catnames);
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else
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for n=1:length(grouporder)
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if isnumeric(data.(grouporder{n}))
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catnames = [catnames grouporder{n}];
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end
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end
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end
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for n=1:length(catnames)
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thisData = data.(catnames{n});
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violins(n) = Violin({thisData}, n, varargin{:});
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end
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set(gca, 'XTick', 1:length(catnames), 'XTickLabels', catnames);
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set(gca,'Box','on');
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return
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elseif iscell(data) && length(data(:))==2 % cell input
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if not(size(data{1},2)==size(data{2},2))
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error('The two input data matrices have to have the same number of columns');
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end
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elseif iscell(data) && length(data(:))>2 % cell input
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error('Up to two datasets can be compared');
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elseif isnumeric(data) % numeric input
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% 1D data, one category for each data point
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if hascategories && numel(data) == numel(cats)
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if isempty(grouporder)
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cats = categorical(cats);
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else
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cats = categorical(cats, grouporder);
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end
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catnames = (unique(cats)); % this ignores categories without any data
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catnames_labels = {};
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for n = 1:length(catnames)
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thisCat = catnames(n);
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catnames_labels{n} = char(thisCat);
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thisData = data(cats == thisCat);
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violins(n) = Violin({thisData}, n, varargin{:});
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end
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set(gca, 'XTick', 1:length(catnames), 'XTickLabels', catnames_labels);
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set(gca,'Box','on');
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return
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else
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data = {data};
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end
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end
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% 1D data, no categories
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if not(hascategories) && isvector(data{1})
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violins = Violin(data, 1, varargin{:});
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set(gca, 'XTick', 1);
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% 2D data with or without categories
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elseif ismatrix(data{1})
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for n=1:size(data{1}, 2)
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thisData = cellfun(@(x)x(:,n),data,'UniformOutput',false);
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violins(n) = Violin(thisData, n, varargin{:});
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end
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set(gca, 'XTick', 1:size(data{1}, 2));
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if hascategories && length(cats) == size(data{1}, 2)
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set(gca, 'XTickLabels', cats);
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end
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end
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set(gca,'Box','on');
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end
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