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241 lines
8.9 KiB
Matlab
241 lines
8.9 KiB
Matlab
%% |boundedline.m|: line with shaded error/confidence bounds
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% Author: Kelly Kearney
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%
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% This repository includes the code for the |boundedline.m| Matlab function
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% and the accompanying |outlinebounds.m| function, along with all dependent
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% functions required to run them.
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%
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% The |boundedline| function allows a user to easily plot and line with a
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% shaded patch around it. Ths sort of plot is often used to indicate
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% uncertainty intervals or error bounds around a line.
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%
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%% Getting started
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%
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% *Prerequisites*
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%
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% This function requires Matlab R14 or later.
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%
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% *Downloading and installation*
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%
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% This code can be downloaded from <https://github.com/kakearney/boundedline-pkg/ Github>
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% or the
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% <http://www.mathworks.com/matlabcentral/fileexchange/27485-boundedline-m
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% MatlabCentral File Exchange>. The File Exchange entry is updated daily
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% from the GitHub repository.
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%
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% *Matlab Search Path*
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%
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% The following folders need to be added to your Matlab Search path (via
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% |addpath|, |pathtool|, etc.):
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%
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% boundedline-pkg/Inpaint_nans
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% boundedline-pkg/boundedline
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% boundedline-pkg/catuneven
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% boundedline-pkg/singlepatch
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%% Syntax
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%
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% |boundedline(x, y, b)| plots a line with coordinates given by
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% |x| and |y|, surrounded by a patch extending a certain distance |b|
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% above/below that line. The dimensions of the |x|, |y|, and |b| arrays
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% can vary to allow for multiple lines to be plotted at once, and for
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% patch bounds to be either constant or varying along the length of the
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% line. See function header help for full details of these variations.
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%
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% |boundedline(..., 'alpha')| renders the bounded area patch using a
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% partially-transparent patch the same color as the corresponding line(s).
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% If not included, the bounded area will use a fully-opaque patch in a
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% lighter shade of the corresponding line color.
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%
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% |boundedline(..., 'transparency', transp)| indicates the
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% tranparency or intensity of the bounds patch, using a scalar between 0
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% and 1. Default is 0.2.
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%
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% |boundedline(..., 'orientation', orient)| indicates the orientation of
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% the bounds. Orientation can be either |'vert'| for vertical (y-direction)
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% bounds, or |'horiz'| for horizontal (x-direction) bounds. Default is
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% |'vert'|.
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%
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% |boundedline(..., 'nan', nanflag)| indicates how the bounds patch should
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% handle NaNs in the line coordinates or bounds values. Options are
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% |'fill'|, to smooth over the gap using neighboring values, |'gap'| to
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% leave a blank space in the patch at those points, or |'remove'| to drop
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% the NaN-points entirely, leading to linear interpolation of the gap in
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% the patch. See examples below for more details on these options.
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%
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% |boundedline(..., 'cmap', cmap)| colors the lines (in order of plotting)
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% acording to the colors in this n x 3 colormap array, overriding any
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% linespec or default colors.
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%
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% |boundedline(..., ax)| plots the bounded line to the axis indicated by
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% handle |ax|. If not included, the current axis is used.
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%
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% |[hl, hp] = boundedline(...)| returns the handles the resulting line
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% and patch object(s).
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%
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% |hout = outlinebounds(hl, hp)| adds an outline to the bounds patch
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% generated by |boundedline|, returning the handle of the resulting line
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% object in |hout|.
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%
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% Full details of all input and output variables for both functions can be
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% accessed via the |help| function.
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%% Example 1: Plotting lines using various syntax options
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%
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% This example builds the 4-panel example image used on the MatlabCentral
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% File Exchange, which shows several different methods for supplying line
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% coordinates, bounds coordinates, and shading options.
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%
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% The first axis plots two lines using the LineSpec option for input, which
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% allows yoy to set line color, line color, and marker type for each line.
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% The bounds on the first line vary over x, while the bounds on the second
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% line are constant for all x. An outline is added to the bounds so the
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% overlapping region can be seen more clearly.
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x = linspace(0, 2*pi, 50);
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y1 = sin(x);
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y2 = cos(x);
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e1 = rand(size(y1))*.5+.5;
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e2 = [.25 .5];
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ax(1) = subplot(2,2,1);
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[l,p] = boundedline(x, y1, e1, '-b*', x, y2, e2, '--ro');
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outlinebounds(l,p);
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title('Opaque bounds, with outline');
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axis tight;
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%%
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% For our second axis, we use the same 2 lines, and this time assign
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% x-varying bounds to both lines. Rather than using the LineSpec syntax,
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% this example uses the default color order to assign the colors of the
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% lines and patches. I also turn on the |'alpha'| option, which renders
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% the patch with partial transparency.
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ax(2) = subplot(2,2,2);
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boundedline(x, [y1;y2], rand(length(y1),2,2)*.5+.5, 'alpha');
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title('Transparent bounds');
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axis tight;
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%%
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% The bounds can also be assigned to a horizontal orientation, for a case
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% where the x-axis represents the dependent variable. In this case, the
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% scalar error bound value applies to both lines and both sides of the
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% lines.
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ax(3) = subplot(2,2,3);
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boundedline([y1;y2], x, e1(1), 'orientation', 'horiz')
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title('Horizontal bounds');
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axis tight;
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%%
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% Rather than use a LineSpec or the default color order, a colormap array
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% can be used to assign colors. In this case, increasingly-narrower bounds
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% are added on top of the same line.
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ax(4) = subplot(2,2,4);
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boundedline(x, repmat(y1, 4,1), permute(0.5:-0.1:0.2, [3 1 2]), ...
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'cmap', cool(4), ...
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'transparency', 0.5);
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title('Multiple bounds using colormap');
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set(ax([1 2 4]), 'xlim', [0 2*pi]);
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set(ax(3), 'ylim', [0 2*pi]);
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axis tight;
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%% Example 2: Filling gaps
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%
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% If you plot a line with one or more NaNs in either the |x| or |y| vector,
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% the NaN location is rendered as a missing marker with a gap in the line.
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% However, the |patch| command does not handle NaNs gracefully; it simply
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% fails to show the patch at all if any of the coordinates include NaNs.
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%
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% Because of this, the expected behavior of the patch part of boundedline
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% when confronted with a NaN in either the bounds array (|b|) or the
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% x/y-coordinates of the line (which are used to calculate the patch
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% coordinates) is ambiguous. I offer a few options.
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%
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% Before I demonstrate the options, I'll create a dataset that has a few
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% different types of gaps:
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x = linspace(0, 2*pi, 50);
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y = sin(x);
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b = [ones(size(y))*0.2; rand(size(y))*.5+.5]';
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y(10) = NaN; % NaN in the line but not bounds
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b(20,1) = NaN; % NaN in lower bound but not line
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b(30,2) = NaN; % NaN in upper bound but not line
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b(40,:) = NaN; % NaN in both sides of bound but not line
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%%
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% Here's what that looks like in an errorbar plot.
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figure;
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he = errorbar(x,y,b(:,1), b(:,2), '-bo');
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line([x([10 20 30 40]); x([10 20 30 40])], [ones(1,4)*-2;ones(1,4)*2], ...
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'color', ones(1,3)*0.5, 'linestyle', ':');
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text(x(10), sin(x(10))-0.2, {'\uparrow','Line','gap'}, 'vert', 'top', 'horiz', 'center');
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text(x(20), sin(x(20))-0.2, {'\uparrow','Lower','bound','gap'}, 'vert', 'top', 'horiz', 'center');
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text(x(30), sin(x(30))-0.2, {'\uparrow','Upper','bound','gap'}, 'vert', 'top', 'horiz', 'center');
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text(x(40), sin(x(40))-0.2, {'\uparrow','Two-sided','bound','gap'}, 'vert', 'top', 'horiz', 'center');
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axis tight equal;
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%%
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% The default method for dealing with NaNs in boundedline is to leave the
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% gap in the line, but smooth over the gap in the bounds based on the
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% neighboring points. This option can be nice if you only have one or two
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% missing points, and you're not interested in emphasizing those gaps in
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% your plot:
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delete(he);
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[hl,hp] = boundedline(x,y,b,'-bo', 'nan', 'fill');
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ho = outlinebounds(hl,hp);
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set(ho, 'linestyle', ':', 'color', 'r', 'marker', '.');
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%%
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% I've added bounds outlines in a contrasting color so you can see how I'm
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% handling individual points.
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%
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% The second option leaves a full gap in the patch for any NaN. I
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% considered allowing one-sided gaps, but couldn't think of a good way to
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% distinguish a gap from a zero-valued bound. I'm open to suggestions if
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% you have any (email me).
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delete([hl hp ho]);
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[hl,hp] = boundedline(x,y,b,'-bo', 'nan', 'gap');
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ho = outlinebounds(hl,hp);
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set(ho, 'linestyle', ':', 'color', 'r', 'marker', '.');
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%%
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% The final option removes points from the patch that are NaNs. The visual
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% result is very similar to the fill option, but the missing points are
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% apparent if you plot the bounds outlines.
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delete([hl hp ho]);
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[hl,hp] = boundedline(x,y,b,'-bo', 'nan', 'remove');
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ho = outlinebounds(hl,hp);
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set(ho, 'linestyle', ':', 'color', 'r', 'marker', '.');
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%% Contributions
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% Community contributions to this package are welcome!
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%
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% To report bugs, please submit
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% <https://github.com/kakearney/boundedline-pkg/issues an issue> on GitHub and
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% include:
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%
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% * your operating system
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% * your version of Matlab and all relevant toolboxes (type |ver| at the Matlab command line to get this info)
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% * code/data to reproduce the error or buggy behavior, and the full text of any error messages received
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%
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% Please also feel free to submit enhancement requests, or to send pull
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% requests (via GitHub) for bug fixes or new features.
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%
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% I do monitor the MatlabCentral FileExchange entry for any issues raised
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% in the comments, but would prefer to track issues on GitHub.
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%
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