From f7cae5ac4ae6ac134337cbc7bb9af291a5d471df Mon Sep 17 00:00:00 2001
From: dleebhsai <dlee@bhsai.org>
Date: Mon, 22 Jan 2018 10:17:10 -0500
Subject: [PATCH]

---
 .../Lineage/Tree/getTreeLenDist.m             | 99 +++++++++++++++++++
 Src/CommonTools/makeStrPattern.m              | 32 ++++++
 2 files changed, 131 insertions(+)
 create mode 100644 Src/AnalysisTools/Lineage/Tree/getTreeLenDist.m
 create mode 100644 Src/CommonTools/makeStrPattern.m

diff --git a/Src/AnalysisTools/Lineage/Tree/getTreeLenDist.m b/Src/AnalysisTools/Lineage/Tree/getTreeLenDist.m
new file mode 100644
index 0000000..bf41f62
--- /dev/null
+++ b/Src/AnalysisTools/Lineage/Tree/getTreeLenDist.m
@@ -0,0 +1,99 @@
+%getTrunkLenDist will get the trunk length distributions. 
+
+function getTreeLenDist()
+FileList = openFileDialog('.csv', 'Open csv files', 'multiselect', 'on');
+for f = 1:length(FileList)
+	getTreeLenDist_Local(FileList{f});
+end
+
+function getTreeLenDist_Local(InFileName)
+
+[VDJdata, VDJheader, FileName, FilePath] = openSeqData(InFileName);
+[H, ~, Chain] = getAllHeaderVar(VDJheader);
+
+if strcmpi(Chain, 'none')
+    for j = [3:10 12:length(VDJheader)]
+        VDJheader{j} = ['H-' VDJheader{j}];
+    end
+    H = getAllHeaderVar(VDJheader);
+end
+
+GrpNum = cell2mat(VDJdata(:, H.GrpNumLoc));
+UnqGrpNum = unique(GrpNum);
+
+LenStats = zeros(length(UnqGrpNum), 7); %GrpCt, CDR3len, SeqLen, MinMiss, MinTrunkLen%, MaxMiss, MaxTrunkLen%
+for j = 1:length(UnqGrpNum)
+    Idx = find(UnqGrpNum(j) == GrpNum);
+    RefSeq = VDJdata{Idx(1), H.RefSeqLoc};
+    CDR3Len = VDJdata{Idx(1), H.CDR3Loc(2)};
+    if ischar(CDR3Len)
+        CDR3Len = str2double(CDR3Len);
+    end
+    MaxMissCt = -1;
+    for k = 1:length(Idx)
+        Seq = VDJdata{Idx(k), H.SeqLoc};
+        MissCt = sum(~((Seq == RefSeq) | Seq == 'X' | RefSeq == 'X'));
+        if k == 1
+            MinMissCt = MissCt;
+        end
+        if MissCt > MaxMissCt
+            MaxMissCt = MissCt;
+        end
+    end
+    LenStats(j, :) = [length(Idx) CDR3Len  length(RefSeq)  MinMissCt  MinMissCt/length(RefSeq) MaxMissCt MaxMissCt/length(RefSeq)];
+end
+
+%For CDF
+
+%Remove singletones
+LenStats(LenStats(:, 1) == 1, :) = [];
+
+%Lowerbound cdf
+MinSHM = sort(LenStats(:,5));
+MinY = [1:length(MinSHM)]/length(MinSHM);
+
+%Upperbound cdf
+MaxSHM = sort(LenStats(:,7));
+MaxY = [1:length(MaxSHM)]/length(MaxSHM);
+
+plot(MinSHM, MinY, 'b', MaxSHM, MaxY, 'r', 'LineWidth', 1);
+
+DotLoc = find(FileName == '.');
+title(strrep(FileName(1:DotLoc(1)-1), '_', '\_'));
+
+xlabel('% mutation');
+ylabel('clonotype frequency');
+resizeSubplots(gca);
+% 
+% OutFileName = fullfile(FilePath, [FileName(1:DotLoc(end)-1), 'TreeLenDist.png']);
+% savePlot(gcf, 'SaveAs', OutFileName, 'Format', 'png');
+% % 
+% 
+% 
+% %For histograms
+% Bins = 0.00:1/125:0.15; 
+% 
+% Nmin = histc(LenStats(:, end-2), Bins);
+% Nmax = histc(LenStats(:, end), Bins);
+% X = repelem(Bins, [1 2*ones(1, numel(Bins)-2) 3]);
+% Ymin = repelem(Nmin, 2*ones(1, numel(Bins)));
+% Ymax = repelem(Nmax, 2*ones(1, numel(Bins)));
+% Lx = plot(X, Ymin, 'b', X, Ymax, 'r');
+% Lx(1).LineWidth = 2;
+% Lx(2).LineWidth = 2;
+% 
+% DotLoc = find(FileName == '.');
+% 
+% 
+% title(strrep(FileName(1:DotLoc(1)-1), '_', '\_'));
+% 
+% BinTxt = cellfun(@(x)sprintf('%0.1f', x*100), num2cell(Bins), 'UniformOutput', false);
+% 
+% set(gca, 'XTickLabel', BinTxt(1:3:end), 'XTick', Bins(1:3:end), 'fontsize', 16, 'linewidth', 1);
+% xlabel('% mutation');
+% ylabel('clonotype frequency');
+% resizeSubplots(gca);
+xlim([0 0.3]);
+OutFileName = fullfile(FilePath, [FileName(1:DotLoc(end)-1), 'TreeLenDist.png']);
+savePlot(gcf, 'SaveAs', OutFileName, 'Format', 'png');
+
diff --git a/Src/CommonTools/makeStrPattern.m b/Src/CommonTools/makeStrPattern.m
new file mode 100644
index 0000000..2c91db8
--- /dev/null
+++ b/Src/CommonTools/makeStrPattern.m
@@ -0,0 +1,32 @@
+%makeStrPattern is used to make a string like 'a,b,c,d,f' for use in repmat
+%or any function required a string format.
+%
+%  Pattern = makeStrPattern(Str, Delimiter)  
+%
+%  INPUT
+%    Str: cell array of char, or a char (each letter gets separated)
+%    Delimiter: delimiter to use to separate the Str elements
+%
+%  OUTPUT
+%    Pattern: a char with alternating Str elements and Delimiter
+%
+%  EXAMPLE
+%    Str = {'a' 'b' 'c'};
+%    Delimiter = ',';
+%    Pattern = makeStrPattern(Str, Delimiter);
+%    Pattern = makeStrPattern([Str{:}], Delimiter);
+%    Pattern = 
+%       'a,b,c'
+
+function Pattern = makeStrPattern(Str, Delimiter)
+if ~ischar(Delimiter)
+    error('%s: Delimiter should be a char.')
+end
+if ischar(Str)
+    Pattern = repmat(Delimiter, 1, length(Str)*2-1);
+    Pattern(1:2:end) = Str;
+elseif iscell(Str) && all(cellfun(@ischar, Str))
+    Pattern = [sprintf(['%s' Delimiter], Str{1:end-1}) Str{end}];
+else
+    error('%s: Str should be a cell array of char or a char.')
+end
\ No newline at end of file