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change_gene_symbols_whole_brain.m
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change_gene_symbols_whole_brain.m
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function change_gene_symbols_wb(MarkerSize, FontSize, MultiCol)
% ChangeGeneSymbols(MarkerSize, FontSize, nPerCol);
%
% changes gene symbols so in situ plots look nice.
% MarkerSize defaults to 6 - if 0, won't change existing sizes
%
% FontSize is font size for legend
%
% nPerCol says how many legend entries per column (0 for one-column)
%
% Kenneth D. Harris, 29/3/17
% GPL 3.0 https://www.gnu.org/licenses/gpl-3.0.en.html
if nargin<1 || isempty(MarkerSize)
MarkerSize = 6;
end
if nargin<2 || isempty(FontSize)
FontSize = 5;
end
if nargin<3
MultiCol = 49;
end
% colors
Astrocytes = hsv2rgb([0 1 1]); % red
Ependymal = hsv2rgb([1/6 1 1]); % yellow
Neurons = hsv2rgb([2/6 1 1]); % green
Immune = hsv2rgb([3/6 1 1]); % cyan
Oligos = hsv2rgb([4/6 1 1]); % blue
Vascular = hsv2rgb([5/6 1 1]); % magenta
Neurons13 = Neurons;
Neurons12 = Neurons;
Neurons11 = Neurons;
Neurons10 = Neurons;
Neurons9 = Neurons;
Neurons8 = Neurons;
Neurons7 = Neurons;
Neurons6 = Neurons;
Neurons5 = Neurons;
Neurons4 = Neurons;
Neurons3 = Neurons;
Neurons2 = Neurons;
Neurons1 = Neurons;
Astrocytes1 = Astrocytes;
Oligos1 = Oligos;
Immune1 = Immune;
Ependymal1 = Ependymal;
Ependymal2 = Ependymal;
Vascular1 = Vascular;
Vascular2 = Vascular;
% All symbols: +o*.xsd^v<>ph - have them in that order to not get confused
New_symbols = {...
'1500015O10Rik', Ependymal, '*'; ...
'2900079G21Rik', Neurons, '*'; ...
'6330403K07Rik', Neurons, '.'; ...
'A230065H16Rik', Neurons, '+'; ...
'Abi3bp', Neurons, 'x'; ...
'Agrp', Neurons, 'o'; ...
'Apoe', Immune, '*'; ...
'Aqp4', Astrocytes, '*'; ...
'Arpp21', Neurons, 's'; ...
'Asb4', Neurons, 'd'; ...
'Asic2', Neurons, '>'; ...
'Atp1a2', Astrocytes, '.'; ...
'Atp1a3', Neurons, 'v'; ...
'Atp1b1', Neurons, '<'; ...
'Avp', Neurons, '^'; ...
'Bcl11a', Neurons, 'p'; ...
'Bex1', Neurons, 'h'; ...
'Bok', Vascular, '*'; ...
'C1ql1', Oligos, '*'; ...
'C1ql3', Neurons1, '*'; ...
'Cabp7', Neurons1, '.'; ...
'Cadm1', Neurons1, '+'; ...
'Calca', Neurons1, 'x'; ...
'Calm2', Neurons1, 'o'; ...
'Caly', Neurons1, 's'; ...
'Camk2n1', Neurons1, 'd'; ...
'Camk4', Neurons1, '>'; ...
'Camkv', Neurons1, 'v'; ...
'Cartpt', Neurons1, '<'; ...
'Cbln1', Neurons1, '^'; ...
'Ccnd2', Ependymal, '.'; ...
'Cd24a', Neurons1, 'p'; ...
'Cdhr1', Neurons1, 'h'; ...
'Celf2', Neurons2, '*'; ...
'Chd3os', Neurons2, '.'; ...
'Ckb', Astrocytes, '+'; ...
'Cldn5', Vascular, '.'; ...
'Cnih2', Neurons2, '+'; ...
'Cpe', Astrocytes, 'x'; ...
'Cplx1', Neurons2, 'x'; ...
'Cpne4', Neurons2, 'o'; ...
'Crabp1', Neurons2, 's'; ...
'Cspg5', Astrocytes, 'o'; ...
'Ctgf', Vascular, '+'; ...
'Ctxn3', Neurons2, 'd'; ...
'Dbi', Ependymal, '+'; ...
'Dcn', Vascular, 'x'; ...
'Ddn', Neurons2, '>'; ...
'Diablo', Neurons2, 'v'; ...
'Dlk1', Neurons2, '<'; ...
'Dlx1', Neurons2, '^'; ...
'Dlx2', Neurons2, 'p'; ...
'Dlx6os1', Neurons2, 'h'; ...
'Dmkn', Ependymal, 'x'; ...
'Doc2g', Neurons3, '*'; ...
'Drd1', Ependymal, 'o'; ...
'Ebf1', Vascular, 'o'; ...
'Ecel1', Neurons3, '.'; ...
'Etv1', Oligos, '.'; ...
'Fabp7', Astrocytes, 's'; ...
'Fam216b', Ependymal, 's'; ...
'Fgf13', Neurons3, '+'; ...
'Fkbp1b', Neurons3, 'x'; ...
'Fndc5', Neurons3, 'o'; ...
'Foxp2', Neurons3, 's'; ...
'Fth1', Oligos, '+'; ...
'Fxyd2', Neurons3, 'd'; ...
'Fxyd6', Neurons3, '>'; ...
'Fxyd7', Neurons3, 'v'; ...
'Gad2', Neurons3, '<'; ...
'Gadd45g', Ependymal, 'd'; ...
'Gal', Neurons3, '^'; ...
'Gap43', Neurons3, 'p'; ...
'Gata2', Vascular, 's'; ...
'Gfap', Astrocytes, 'd'; ...
'Gfra3', Neurons3, 'h'; ...
'Gm17750', Ependymal, '>'; ...
'Gm2694', Neurons4, '*'; ...
'Gm27199', Neurons4, '.'; ...
'Gm3764', Astrocytes, '>'; ...
'Gm42418', Ependymal, 'v'; ...
'Gm5741', Neurons4, '+'; ...
'Gnrh1', Neurons4, 'x'; ...
'Gpm6a', Neurons4, 'o'; ...
'Gpr88', Neurons4, 's'; ...
'Gria2', Neurons4, 'd'; ...
'Grin2a', Neurons4, '>'; ...
'Grin2b', Neurons4, 'v'; ...
'H3f3a', Vascular, 'd'; ...
'H3f3b', Vascular, '>'; ...
'Hcn1', Neurons4, '<'; ...
'Hoxa5', Neurons4, '^'; ...
'Hoxa7', Ependymal, '<'; ...
'Hoxa9', Ependymal, '^'; ...
'Hoxb5', Neurons4, 'p'; ...
'Hoxb6', Neurons4, 'h'; ...
'Hoxb7', Neurons5, '*'; ...
'Hoxb8', Neurons5, '.'; ...
'Hoxb9', Neurons5, '+'; ...
'Hoxc10', Ependymal, 'p'; ...
'Hoxc8', Ependymal, 'h'; ...
'Hpca', Neurons5, 'x'; ...
'Hpcal1', Neurons5, 'o'; ...
'Htr1f', Neurons5, 's'; ...
'Igf1', Vascular, 'v'; ...
'Igfbp2', Ependymal1, '*'; ...
'Igfbp4', Vascular, '<'; ...
'Igfbp6', Vascular, '^'; ...
'Igfbpl1', Neurons5, 'd'; ...
'Impact', Neurons5, '>'; ...
'Isl1', Neurons5, 'v'; ...
'Itm2b', Immune, '.'; ...
'Junb', Immune, '+'; ...
'Kcnc1', Neurons5, '<'; ...
'Kcnh3', Neurons5, '^'; ...
'Kcnip2', Neurons5, 'p'; ...
'Lbx1', Neurons5, 'h'; ...
'Ldhb', Neurons6, '*'; ...
'Lhx1os', Neurons6, '.'; ...
'Lhx2', Astrocytes, 'v'; ...
'Lix1', Neurons6, '+'; ...
'Lpl', Vascular, 'p'; ...
'Lsamp', Neurons6, 'x'; ...
'Ly6g6e', Neurons6, 'o'; ...
'Ly6h', Neurons6, 's'; ...
'Malat1', Oligos, 'x'; ...
'Marcks', Oligos, 'o'; ...
'Matn4', Oligos, 's'; ...
'Mbp', Oligos, 'd'; ...
'Mef2c', Neurons6, 'd'; ...
'Meg3', Neurons6, '>'; ...
'Meis2', Neurons6, 'v'; ...
'Mgp', Vascular, 'h'; ...
'Mlc1', Ependymal1, '.'; ...
'Mobp', Oligos, '>'; ...
'Mpz', Neurons6, '<'; ...
'Msx1', Ependymal1, '+'; ...
'Mt1', Astrocytes, '<'; ...
'Mt3', Ependymal1, 'x'; ...
'mt-Atp6', Neurons6, '^'; ...
'mt-Co3', Neurons6, 'p'; ...
'mt-Cytb', Ependymal1, 'o'; ...
'mt-Nd1', Neurons6, 'h'; ...
'Myl1', Neurons7, '*'; ...
'Myl4', Vascular1, '*'; ...
'Myl9', Vascular1, '.'; ...
'Nap1l5', Neurons7, '.'; ...
'Ndufa4', Neurons7, '+'; ...
'Ndufa4l2', Vascular1, '+'; ...
'Nefl', Neurons7, 'x'; ...
'Nefm', Neurons7, 'o'; ...
'Nek7', Neurons7, 's'; ...
'Neurod1', Neurons7, 'd'; ...
'Neurod2', Neurons7, '>'; ...
'Nfib', Ependymal1, 's'; ...
'Nfix', Ependymal1, 'd'; ...
'Ngfr', Neurons7, 'v'; ...
'Nnat', Ependymal1, '>'; ...
'Nppb', Neurons7, '<'; ...
'Nppc', Neurons7, '^'; ...
'Nptx1', Neurons7, 'p'; ...
'Nrgn', Neurons7, 'h'; ...
'Nrsn1', Neurons8, '*'; ...
'Nrxn1', Neurons8, '.'; ...
'Nrxn3', Neurons8, '+'; ...
'Ntn1', Vascular1, 'x'; ...
'Nts', Neurons8, 'x'; ...
'Ntsr2', Astrocytes, '^'; ...
'Olfm1', Neurons8, 'o'; ...
'Olig1', Oligos, 'v'; ...
'Olig2', Oligos, '<'; ...
'Opcml', Neurons8, 's'; ...
'Ostf1', Vascular1, 'o'; ...
'Otp', Neurons8, 'd'; ...
'Oxt', Neurons8, '>'; ...
'Pantr1', Astrocytes, 'p'; ...
'Pax6', Ependymal1, 'v'; ...
'Pcdh7', Oligos, '^'; ...
'Pcdh8', Neurons8, 'v'; ...
'Pcp2', Neurons8, '<'; ...
'Pcp4l1', Ependymal1, '<'; ...
'Pde10a', Neurons8, '^'; ...
'Pdgfra', Vascular1, 's'; ...
'Pdyn', Neurons8, 'p'; ...
'Pdzk1ip1', Vascular1, 'd'; ...
'Pgam2', Neurons8, 'h'; ...
'Pkib', Neurons9, '*'; ...
'Pla2g5', Ependymal1, '^'; ...
'Plcd4', Ependymal1, 'p'; ...
'Pmch', Neurons9, '.'; ...
'Postn', Vascular1, '>'; ...
'Ppp1r1b', Ependymal1, 'h'; ...
'Ppp3ca', Neurons9, '+'; ...
'Prkcd', Neurons9, 'x'; ...
'Prok2', Neurons9, 'o'; ...
'Ptgds', Vascular1, 'v'; ...
'Ptma', Vascular1, '<'; ...
'Ptn', Vascular1, '^'; ...
'Pura', Neurons9, 's'; ...
'Ramp1', Ependymal2, '*'; ...
'Ramp3', Neurons9, 'd'; ...
'Rarres1', Neurons9, '>'; ...
'Rbfox1', Neurons9, 'v'; ...
'Rbp4', Ependymal2, '.'; ...
'Resp18', Neurons9, '<'; ...
'Rgs5', Vascular1, 'p'; ...
'Rln3', Neurons9, '^'; ...
'Rora', Neurons9, 'p'; ...
'Rpl26', Neurons9, 'h'; ...
'Rprm', Neurons10, '*'; ...
'Rprml', Neurons10, '.'; ...
'Rps2', Neurons10, '+'; ...
'Rsrp1', Neurons10, 'x'; ...
'S100a6', Neurons10, 'o'; ...
'Sall3', Ependymal2, '+'; ...
'Scg2', Neurons10, 's'; ...
'Scg5', Neurons10, 'd'; ...
'Scn1b', Neurons10, '>'; ...
'Sdk2', Neurons10, 'v'; ...
'Sepw1', Neurons10, '<'; ...
'Serpinb1b', Neurons10, '^'; ...
'Shisa8', Neurons10, 'p'; ...
'Six3', Neurons10, 'h'; ...
'Sla', Immune, 'x'; ...
'Slc17a6', Neurons11, '*'; ...
'Slc17a7', Neurons11, '.'; ...
'Slc1a2', Astrocytes, 'h'; ...
'Slc32a1', Neurons11, '+'; ...
'Slc6a11', Astrocytes1, '*'; ...
'Slc6a17', Neurons11, 'x'; ...
'Slc6a2', Neurons11, 'o'; ...
'Slc6a5', Neurons11, 's'; ...
'Slco5a1', Neurons11, 'd'; ...
'Sncb', Neurons11, '>'; ...
'Snhg11', Neurons11, 'v'; ...
'Sp9', Neurons11, '<'; ...
'Sparc', Vascular1, 'h'; ...
'Sparcl1', Astrocytes1, '.'; ...
'Spp1', Vascular2, '*'; ...
'Spp2', Ependymal2, 'x'; ...
'Syndig1', Neurons11, '^'; ...
'Syt2', Neurons11, 'p'; ...
'Syt4', Neurons11, 'h'; ...
'Tcap', Neurons12, '*'; ...
'Tcf4', Oligos, 'p'; ...
'Tcf7l2', Oligos, 'h'; ...
'Tecr', Neurons12, '.'; ...
'Tfap2b', Neurons12, '+'; ...
'Thy1', Neurons12, 'x'; ...
'Tlx3', Neurons12, 'o'; ...
'Tmsb4x', Vascular2, '.'; ...
'Tph2', Neurons12, 's'; ...
'Trh', Neurons12, 'd'; ...
'Tshz1', Neurons12, '>'; ...
'Tshz2', Neurons12, 'v'; ...
'Ttr', Ependymal2, 'o'; ...
'Tuba1a', Neurons12, '<'; ...
'Ubb', Neurons12, '^'; ...
'Ube2c', Oligos1, '*'; ...
'Uncx', Neurons12, 'p'; ...
'Vamp1', Neurons12, 'h'; ...
'Vgf', Neurons13, '*'; ...
'Vsnl1', Neurons13, '.'; ...
'Vstm2b', Neurons13, '+'; ...
'Vtn', Vascular2, '+'; ...
'Xist', Oligos1, '.'; ...
'Zbtb20', Ependymal2, 's'; ...
'Zeb2', Oligos1, '+'; ...
'Zic1', Vascular2, 'x'; ...
};
% delete any existing legend
fc = get(gcf, 'Children');
for i=1:length(fc)
if strcmp(get(fc(i), 'UserData'), 'key')
delete(fc(i));
end
end
MainAxes = gca;
n = size(New_symbols,1);
gc = get(MainAxes, 'children');
MyChildren = [];
for i=1:length(gc)
if (strcmp(gc(i).Type, 'line') || strcmp(gc(i).Type, 'scatter')) ...
&& ~isempty(gc(i).DisplayName)
MyChildren = [MyChildren; i];
end
end
DisplayNames = {gc(MyChildren).DisplayName};
% get first word of display name as gene
GeneNames = cell(size(DisplayNames));
for i=1:length(DisplayNames)
GeneNames{i} = strtok(DisplayNames{i});
end
clear h s;
j=1;
Present = [];
for i=1:n
MyGeneName = New_symbols{i,1};
l = find(strcmp(MyGeneName, GeneNames));
if ~isempty(l)
h(j) = gc(MyChildren(l));
if strcmp(h(j).Type, 'line')
set(h(j), 'Color', New_symbols{i,2});
elseif strcmp(h(j).Type, 'scatter')
set(h(j), 'CData', New_symbols{i,2});
end
set(h(j), 'Marker', New_symbols{i,3});
if MarkerSize>0
if strcmp(gc(l).Type, 'line')
set(h(j), 'MarkerSize', MarkerSize);
elseif strcmp(gc(l).Type, 'scatter')
set(h(j), 'SizeData', MarkerSize);
end
end
Present(j) = i;
j=j+1;
end
end
other_h = setdiff(gc(MyChildren), h);
other_symbols = {other_h.DisplayName};
all_h = [h(:); other_h(:)];
all_sym = {New_symbols{Present,1}, other_symbols{:}};
% lh = legend([h(:); other_h(:)], ...
% {New_symbols{s,1}, other_symbols{:}}, ...
% 'color', 'k', 'textcolor', 'w', 'fontsize', FontSize);
% set(lh, 'color', 'k');
%
% return;
if MultiCol==0
lh = legend(all_h, all_sym, 'color', 'k', 'textcolor', 'w', 'fontsize', FontSize);
set(lh, 'color', 'k');
else
ah = axes('Position', [.925 .13 .05 .8]);
set(ah, 'color', 'k'); cla; hold on; box off
set(ah, 'UserData', 'key');
for j=1:length(Present)
i = Present(j);
plot(ceil(j/MultiCol)+.1, mod(j-1,MultiCol), New_symbols{i,3}, 'Color', New_symbols{i,2});
text(ceil(j/MultiCol)+.3, mod(j-1,MultiCol), New_symbols{i,1}, 'color', 'w', 'fontsize', FontSize);
end
ylim([-1 MultiCol]);
set(ah, 'xtick', []);
set(ah, 'ytick', []);
set(ah, 'ydir', 'reverse');
end
% for c=1:nCols
% rr=((c-1)*50 + 1):min(c*50, length(all_h));
% if c==1
% ah(c) = gca;
% lh(c) = legend(all_h(rr), all_sym(rr), 'color', 'k', 'textcolor', 'w', 'fontsize', FontSize, 'location', 'east');
% set(lh(c), 'color', 'k');
% pos(c,:) = get(lh(c), 'position');
% else
% ah(c) = axes('position',get(gca,'position'), 'visible','off');
% lh(c) = legend(ah(c), all_h(rr), all_sym(rr), 'color', 'k', 'textcolor', 'w', 'fontsize', FontSize, 'location', 'east');
% set(lh(c), 'position', pos(c-1,:) + [1.1 0 0 0]*pos(c-1,3));
% uistack(lh(c), 'top');
% end
% end
% axes(ah(1));
% error('multicolumn not done yet!');
% end
% for i=1:nCols
% first = 1+(i-1)*nCols;
% last = min(i*nCols,length(all_h));
% lh = legend(all_h(first:last), ...
% all_sym{first:last});%, ...
% %'color', 'k', 'textcolor', 'w', 'fontsize', FontSize);
% set(lh, 'color', 'k');
% end
set(gcf, 'color', 'k');
set(gcf, 'InvertHardcopy', 'off');
axes(MainAxes)
uistack(ah, 'top');
end