You can plot each quiver arrow in a loop to individually control the colors. This demo assigns color according to the magnitude of each vector.
% Demo data
[X,Y] = meshgrid(-2:0.2:2);
Z = X .* exp(-X.^2 - Y.^2);
[U,V] = gradient(Z,0.2,0.2);
% Create axes
ax = axes('Color', [.15 .15 .15]);
hold(ax,'on')
box(ax,'on')
% Define the colormap for the quiver arrows.
% cmap can have any number of rows.
cmap = autumn(255);
ax.Colormap = cmap;
% Assign colors based on magnitude of vectors
vectorMagnitude = hypot(U(:),V(:));
% Scale magnitudes to rows of colormap
vecMagNorm = (vectorMagnitude-min(vectorMagnitude))./range(vectorMagnitude);
vecColorIdx = round(vecMagNorm * (size(cmap,1)-1)) + 1;
% Plot the quiver data
for i = 1:numel(Z)
quiver(ax, X(i),Y(i),U(i),V(i), .2, ...
'Color', cmap(vecColorIdx(i),:), 'LineWidth',1)
end
% Set properties for the main axes
axis equal
xlim(ax, [-2 2])
ylim(ax, [-2 2])
% Add colorbar
cb = colorbar(ax);
% Set colorbar range
caxis(ax, [floor(vectorMagnitude(1)), ceil(vectorMagnitude(2))])
% Label the colorbars
ylabel(cb,'Vector magnitude')
