function bh = figure_boxplot(data_input,...
text_label_in,label_xaxis_data_in,text_title_in,label_orientation_choice_in,...
box_color_in,box_lineWidth_in,box_widths_value_in,box_color_transparency_in,...
median_lineWidth_in,median_color_in,...
whisker_value_in,...
outlier_marker_in,outlier_markerSize_in,outlier_marker_edgeWidth_in,outlier_marker_edgeColor_in,outlier_jitter_value_in,...
savefig_in,savefig_name_in,fig_width_cm_in,fig_height_cm_in,...
ylim_min_in,ylim_max_in)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Adaption of MATLAB boxplot function to plot beautiful publication-quality boxplots easily
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Written by: Ahmed Abdul Quadeer
% E-mail: ahmedaq@gmail.com
% Last change: May 29, 2018
% Copyright (c) Ahmed Abdul Quadeer, 2019
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Inputs:
%
% - data_input: Input data
% * N-length cell including data, with each cell having data of one boxplot
% to be compared. G matrix to be used in the default MATLAB "boxplot"
% function is generated accordingly.
% * a matrix of size MxN, where M = no. of observation and N = no. of
% variables. Boxplot is made for each variable (column) of input matrix
%
% - text_label_in: Labels for x-axis and y-axis
% Cell of length 2, with first cell having text of x-axis label and
% second cell having text of y-axis label
%
% - label_xaxis_data_in: Label for each box plot on the x-axis
% N-length cell (containing text) or N-length vector numerical data
%
% - text_title_in: Title of the box plot
% N-length cell (containing text) or N-length vector numerical data
%
% - label_orientation_choice_in: Choice for orientation of boxplot labels
% * 'horizontal' (default) or
% * 'inline' (vertical) suitable for long labels
%
% - box_color_in: Color of boxplots
% Nx3 sized matrix with first row specifying RGB color for the first box
% plot and so on.
%
% - box_lineWidth_in: Width of boxplots outline
% Scalar value
%
% - box_widths_value_in: Width of boxplots
% Scalar value
%
% - box_color_transparency_in: Transparency of box plots
% Scalar value between 0 (transparent) and 1 (opaque)
%
% - median_lineWidth_in: Width of the line representing the median
% Scalar value
%
% - median_color_in: Color of the line representing the median
% 3-length row vector specifying the RGB color
%
% - whisker_value_in: Limit of whiskers
% Scalar value "a" in the definition of whiskers:a * inter-quartile-range
%
% - outlier_marker_in: Marker to represent outliers
% e.g. 'o', 'x', '.', or '+'
%
% - outlier_markerSize_in: Size of the marker representing outliers
% Scalar value
%
% - outlier_marker_edgeWidth_in: Width of the edge (outline) of the marker
% represeting outliers
% Scalar value
%
% - outlier_marker_edgeColor_in: Color of the edge (outline) of the marker
% represeting outliers
% 3-length row vector specifying the RGB color. Black ('k') and white
% ('w') (default) generally are good options.
%
% - outlier_jitter_value_in: Variance of the random noise added to outliers
% for visualization purpose
% Scalar value
%
% - savefig_in: Option to save figure automatically (in png format)
% * 1 - Yes, save the figure
% * 0 - No
%
% - savefig_name_in: Name for the figure file
% Text data
%
% - fig_width_cm_in: Width of the output figure (in cm)
% Scalar value
%
% - fig_height_cm_in: Height of the output figure (in cm)
% Scalar value
%
% - ylim_min_in: Lower limit of y-axis
% Scalar value
%
% - ylim_max_in: Upper limit of y-axis
% Scalar value
%
%
%
% Output: Box plot figure
%
%
%% Basic settings
%%% Font type and size setting %%%
% Using Arial as default because all journals normally require the font to
% be either Arial or Helvetica
set(0,'DefaultAxesFontName','Arial')
set(0,'DefaultTextFontName','Arial')
set(0,'DefaultAxesFontSize',10)
set(0,'DefaultTextFontSize',10)
%%% Color definition %%%
% Using Nature color scheme
% Reason: Because it is really cool!
% Drawback: Only 9 colors
% You can use any other scheme as well, for example check:
% https://ggsci.net/index.html for other journal templates
% color_scheme_npg_hex = ['#E64B35';'#4DBBD5';'#00A087';'#3C5488';....
% '#F39B7F';'#8491B4';'#91D1C2';'#DC0000';'#7E6148';'#B09C85'];
% color_scheme_npg = hex2rgb(color_scheme_npg_hex);
color_scheme_npg = [...
0.9020 0.2941 0.2078; ...
0.3020 0.7333 0.8353; ...
0 0.6275 0.5294; ...
0.2353 0.3294 0.5333; ...
0.9529 0.6078 0.4980; ...
0.5176 0.5686 0.7059; ...
0.5686 0.8196 0.7608; ...
0.8627 0 0; ...
0.4941 0.3804 0.2824; ...
0.6902 0.6118 0.5216 ];
%% Processing with respect to number of input arguments
%Number of boxplots
if iscell(data_input) %if input data is in cell form
no_boxplots = length(data_input);
else %if input data is in matrix form
no_boxplots = size(data_input,2);
end
if no_boxplots>9 || isempty(data_input)
fprintf('\nWarning: The number of box plots to be plotted is greater than colors in the selected scheme. Using one color for all boxes.')
end
%Defaults
box_lineWidth = 0.5;
box_widths_value = 0.3;
if no_boxplots>9
box_color = [0.9020 0.2941 0.2078];
else
box_color = color_scheme_npg(1:no_boxplots,:);
end
%Defaults
box_lineWidth = 0.5;
box_widths_value = 0.3;
box_color = color_scheme_npg(1:no_boxplots,:);
box_color_transparency = 0.7; %faceAlpha
median_lineWidth = 2;
median_color = 'k';
whisker_value = 1.5;
outlier_marker = 'o';
outlier_markerSize = 4;
outlier_marker_edgeWidth = 0.1;
outlier_marker_edgeColor = 'w';
outlier_jitter_value = 0.3;
label_xaxis_data = 1:no_boxplots;
text_label{1} = '';
text_label{2} = '';
text_title = '';
label_orientation_choice = 'horizontal'; %'inline'
savefig = 0;
savefig_name = 'fig_boxplot_noname';
fig_width_cm = 10;
fig_height_cm = 5;
if nargin == 2
text_label = text_label_in;
elseif nargin == 3
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
elseif nargin == 4
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
elseif nargin == 5
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
elseif nargin == 6
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
elseif nargin == 7
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
elseif nargin == 8
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
elseif nargin == 9
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
elseif nargin == 10
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
elseif nargin == 11
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
elseif nargin == 12
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
elseif nargin == 13
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
elseif nargin == 14
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
elseif nargin == 15
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
outlier_marker_edgeWidth = outlier_marker_edgeWidth_in;
elseif nargin == 16
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
outlier_marker_edgeWidth = outlier_marker_edgeWidth_in;
outlier_marker_edgeColor = outlier_marker_edgeColor_in;
elseif nargin == 17
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
outlier_marker_edgeWidth = outlier_marker_edgeWidth_in;
outlier_marker_edgeColor = outlier_marker_edgeColor_in;
outlier_jitter_value = outlier_jitter_value_in;
elseif nargin == 18
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
outlier_marker_edgeWidth = outlier_marker_edgeWidth_in;
outlier_marker_edgeColor = outlier_marker_edgeColor_in;
outlier_jitter_value = outlier_jitter_value_in;
savefig = savefig_in;
elseif nargin == 19
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
outlier_marker_edgeWidth = outlier_marker_edgeWidth_in;
outlier_marker_edgeColor = outlier_marker_edgeColor_in;
outlier_jitter_value = outlier_jitter_value_in;
savefig = savefig_in;
savefig_name = savefig_name_in;
elseif nargin == 20
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
outlier_marker_edgeWidth = outlier_marker_edgeWidth_in;
outlier_marker_edgeColor = outlier_marker_edgeColor_in;
outlier_jitter_value = outlier_jitter_value_in;
savefig = savefig_in;
savefig_name = savefig_name_in;
fig_width_cm = fig_width_cm_in;
elseif nargin == 21
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
outlier_marker_edgeWidth = outlier_marker_edgeWidth_in;
outlier_marker_edgeColor = outlier_marker_edgeColor_in;
outlier_jitter_value = outlier_jitter_value_in;
savefig = savefig_in;
savefig_name = savefig_name_in;
fig_width_cm = fig_width_cm_in;
fig_height_cm = fig_height_cm_in;
elseif nargin == 22
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
outlier_marker_edgeWidth = outlier_marker_edgeWidth_in;
outlier_marker_edgeColor = outlier_marker_edgeColor_in;
outlier_jitter_value = outlier_jitter_value_in;
savefig = savefig_in;
savefig_name = savefig_name_in;
fig_width_cm = fig_width_cm_in;
fig_height_cm = fig_height_cm_in;
ylim_min = ylim_min_in;
elseif nargin == 23
text_label = text_label_in;
label_xaxis_data = label_xaxis_data_in;
text_title = text_title_in;
label_orientation_choice = label_orientation_choice_in;
box_color = box_color_in;
box_lineWidth = box_lineWidth_in;
box_widths_value = box_widths_value_in;
box_color_transparency = box_color_transparency_in;
median_lineWidth = median_lineWidth_in;
median_color = median_color_in;
whisker_value = whisker_value_in;
outlier_marker = outlier_marker_in;
outlier_markerSize = outlier_markerSize_in;
outlier_marker_edgeWidth = outlier_marker_edgeWidth_in;
outlier_marker_edgeColor = outlier_marker_edgeColor_in;
outlier_jitter_value = outlier_jitter_value_in;
savefig = savefig_in;
savefig_name = savefig_name_in;
fig_width_cm = fig_width_cm_in;
fig_height_cm = fig_height_cm_in;
ylim_min = ylim_min_in;
ylim_max = ylim_max_in;
end
%% Preprocessing data for plotting
data = [];
G = [];
if ~iscell(data_input) %if input data is in matrix form
for kk = 1:size(data_input,2)
data_temp = data_input(:,kk);
data = [data data_temp.'];
G = [G kk*ones(1,size(data_input,1))];
end
else %if input data is in cell form
for kk = 1:no_boxplots
data_temp = data_input{kk};
data = [data data_temp(:).'];
G = [G kk*ones(1,length(data_input{kk}))];
end
end
%% Main box plot
% figure;
bh = boxplot(data,G,...
'whisker',whisker_value,'symbol',outlier_marker,...
'color','k','jitter',outlier_jitter_value,...
'labels',label_xaxis_data,...
'widths',box_widths_value,'LabelOrientation',label_orientation_choice);
set(bh,'linewidth',box_lineWidth);
xlabel(text_label{1});
ylabel(text_label{2})
title(text_title)
%% Rotate xaxis labels by 45 degrees and make their font smaller only if
%% labels>10
if length(label_xaxis_data)>10
set(gca,'XTickLabelRotation',45)
xL = xlabel(text_label{1});
ax = ancestor(gca, 'axes');
xrule = ax.XAxis;
xrule.FontSize = 8;
xL.FontSize = 10;
end
%% Coloring each box
h = findobj(gca,'Tag','Box');
if size(box_color,1) ~= 1 %if colors provided for each box
for kk = 1:length(h)
patch(get(h(kk),'XData'),get(h(kk),'YData'),box_color(length(h)-kk+1,:),'FaceAlpha',box_color_transparency);
end
else
for kk = 1:length(h)
patch(get(h(kk),'XData'),get(h(kk),'YData'),box_color,'FaceAlpha',box_color_transparency);
end
end
% Sending patch to back of the figure so that median can be drawn on top of it
set(gca,'children',flipud(get(gca,'children')))
%% Adjusting median
h=findobj(gca,'tag','Median');
for kk = 1:length(h)
h(kk).LineWidth = median_lineWidth;
h(kk).Color = median_color;
end
%% Adjusting outliers
h=findobj(gca,'tag','Outliers');
for kk = 1:length(h)
if size(box_color,1) ~= 1 %if colors provided for each box
h(kk).MarkerFaceColor = box_color(length(h)-kk+1,:); alpha(box_color_transparency)
else
h(kk).MarkerFaceColor = box_color; alpha(box_color_transparency)
end
h(kk).MarkerEdgeColor = outlier_marker_edgeColor;
h(kk).MarkerSize = outlier_markerSize;
h(kk).LineWidth = outlier_marker_edgeWidth;
end
% ylim([ylim_min ylim_max])
%% Further post-processing the figure
set(gca, ...
'Box' , 'off' , ...
'TickDir' , 'out' , ...
'TickLength' , [.01 .01] , ...
'XColor' , [.1 .1 .1], ...
'YColor' , [.1 .1 .1], ...
'XTick' , 1:1:100,...
'LineWidth' , .5 );
%% Saving figure
if savefig == 1
set(gcf,'PaperUnits','centimeters','PaperPosition',[0 0 fig_width_cm fig_height_cm])
print(savefig_name,'-dpng','-r300')
end
Datasets
Models
