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scgeatool.m
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function varargout = scgeatool(sce, varargin)
if usejava('jvm') && ~feature('ShowFigureWindows')
error('MATLAB is in a text mode. This function requires a GUI-mode.');
end
if ~gui.i_installed('stats'), return; end
persistent speciestag
ptimgidx = 1;
ptImgCell = cell(2, 50);
import pkg.*
import gui.*
fx = [];
if nargin < 1
try
fxfun = @gui.sc_splashscreen;
[fx, v1] = fxfun();
catch
fxfun = @gui.sc_simplesplash;
[fx, v1] = fxfun();
end
sce = SingleCellExperiment;
else
if isempty(sce), sce = SingleCellExperiment; end
if ~isa(sce, 'SingleCellExperiment')
error('requires >> sce = SingleCellExperiment(); scgeatool(sce)');
end
v1 = pkg.i_get_versionnum;
end
mfolder = fileparts(mfilename('fullpath'));
p = inputParser;
checkCS = @(x) isempty(x) | size(sce.X, 2) == length(x);
addRequired(p, 'sce', @(x) isa(x, 'SingleCellExperiment'));
addOptional(p, 'c', sce.c, checkCS);
addOptional(p, 's', [], checkCS);
addOptional(p, 'methodid', 1, @isnumeric);
addOptional(p, 'legacy', false, @islogical);
addOptional(p, 'callinghandle', []);
parse(p, sce, varargin{:});
callinghandle = p.Results.callinghandle;
c_in = p.Results.c;
s_in = p.Results.s;
methodid = p.Results.methodid;
legacy = p.Results.legacy;
if legacy
ptImgFile = fullfile(mfolder, 'resources', 'Images', 'ptImgFile_legacy.mat');
else
ptImgFile = fullfile(mfolder, 'resources', 'Images', 'ptImgFile.mat');
end
if exist(ptImgFile, 'file'), load(ptImgFile, 'ptImgCell'); end
f_traj = []; % trajectory curve
ax = []; bx = [];
tmpcelltypev = cell(sce.NumCells, 1);
if ~isempty(c_in), sce.c = c_in; end
if ~isempty(s_in), sce.s = s_in; end
[c, cL] = grp2idx(sce.c);
[FigureHandle] = gui.gui_createmainfigure(v1);
if ~isempty(fx) && isvalid(fx), fxfun(fx,0.2); end
[button1, button2] = gui.gui_createbuttons(FigureHandle, @in_sc_openscedlg);
m_file = createMenus(FigureHandle, 1);
m_edit = createMenus(FigureHandle, 2);
m_view = createMenus(FigureHandle, 3);
m_plot = createMenus(FigureHandle, 4);
m_anno = createMenus(FigureHandle, 5);
m_tool = createMenus(FigureHandle, 6);
m_ntwk = createMenus(FigureHandle, 7);
m_extn = createMenus(FigureHandle, 8);
% m_optn = createMenus(FigureHandle, 9);
if ~isempty(fx) && isvalid(fx), fxfun(fx, 0.4); end
hAx = axes('Parent', FigureHandle, 'Visible', 'off');
% axtoolbar(hAx, 'default');
if ~isempty(sce) && sce.NumCells>0
h = gui.i_gscatter3(sce.s, c, methodid, 1, hAx);
title(hAx, sce.title);
if sce.s>2
rotate3d(hAx,'on');
else
brush(hAx,'on');
end
subtitle(hAx,'[genes x cells]');
else
h = [];
hAx.Toolbar.Visible = 'off';
end
DeftToolbarHandle = uitoolbar('Parent', FigureHandle);
MainToolbarHandle = uitoolbar('Parent', FigureHandle);
UserToolbarHandle = uitoolbar('Parent', FigureHandle);
createPushButtons(FigureHandle);
if ~isempty(fx) && isvalid(fx), fxfun(fx, 0.6); end
pause(0.5);
if ~isempty(fx) && isvalid(fx), fxfun(fx, 0.8); end
if ~isempty(c)
kc = numel(unique(c));
colormap(pkg.i_mycolorlines(kc));
end
if ~isempty(sce) && sce.NumCells>0
in_EnDisableMenu('on');
else
in_EnDisableMenu('off');
end
if ~isempty(sce) && sce.NumCells>0, hAx.Visible="on"; end
createMenus(FigureHandle, 10);
if ~isempty(fx) && isvalid(fx), fxfun(fx, 1.0); end
pause(1);
if ~isempty(fx) && isvalid(fx), set(fx, 'visible', 'off'); end
pause(0.2);
delete(fx);
set(FigureHandle, 'visible', 'on');
if matlab.ui.internal.isUIFigure(FigureHandle), focus(FigureHandle); end
uicontrol(button1);
guidata(FigureHandle, sce);
set(FigureHandle, 'CloseRequestFcn', @in_closeRequest);
if nargout > 0, varargout{1} = FigureHandle; end
if ~ispref('scgeatoolbox', 'useronboardingtoolbar')
gui.gui_userguidingpref(true);
setpref('scgeatoolbox', 'useronboardingtoolbar', true);
end
showuseronboarding = getpref('scgeatoolbox', 'useronboardingtoolbar', false);
if ~showuseronboarding, set(UserToolbarHandle, 'Visible', 'off'); end
if ~exist(ptImgFile, 'file'), save(ptImgFile, 'ptImgCell'); end
% ------------------------
% GUI Making Functions
% ------------------------
% function [FigureHandle] = createMainFigure(v1)
% if ~isempty(v1)
% figname = sprintf('SCGEATOOL v%s', v1);
% else
% figname = 'SCGEATOOL';
% end
% defaultPosition = get(groot, 'DefaultFigurePosition');
% defaultWidth = defaultPosition(3);
% defaultHeight = defaultPosition(4);
% if defaultWidth==560 && defaultHeight==420
% FigureHandle = figure('Name', figname, ...
% 'position', round(1.2*[0, 0, 560, 420]), ...
% 'visible', 'off', 'NumberTitle', 'off', ...
% 'DockControls','off','MenuBar','none','ToolBar','Figure');
% else
% FigureHandle = figure('Name', figname, ...
% 'visible', 'off', 'NumberTitle', 'off', ...
% 'DockControls','off','MenuBar','none','ToolBar','Figure');
% end
% delete(findall(FigureHandle, 'Tag', 'FigureToolBar'));
% movegui(FigureHandle, 'center');
% dt = datacursormode(FigureHandle);
% dt.Enable = 'off';
% dt.UpdateFcn = {@i_myupdatefcnx};
% end
% function [button1, button2]= createButtons(FigureHandle)
% fig_pos = get(FigureHandle, 'Position');
% fig_width = fig_pos(3);
% fig_height = fig_pos(4);
% btn_width = 100;
% btn_height = 25;
% btn_x = (fig_width - btn_width) / 2;
% btn_y = (fig_height - btn_height) / 1.618;
%
% button1 = uicontrol('Parent', FigureHandle,...
% 'Style', 'pushbutton',...
% 'Units', 'pixels',...
% 'Position', [btn_x btn_y btn_width btn_height],...
% 'String', 'Import Data...',...
% 'Callback', @in_sc_openscedlg,...
% 'ButtonDownFcn', @in_sc_openscedlg,...
% 'KeyPressFcn', @in_sc_openscedlg, 'Tooltip','Click or Press i');
%
% button2 = uicontrol('Parent', FigureHandle,...
% 'style','text',...
% 'Units', 'pixels',...
% 'position', [btn_x btn_y+25 btn_width btn_height],...
% 'FontSize', 9,...
% 'string','Ready to explore.');
% set(FigureHandle,'resizefcn',{@gui.gui_myresizefun, button1, button2});
% end
function menus = createMenus(FigureHandle, id)
switch id
case 1
menus = uimenu(FigureHandle, 'Text', '&File');
in_addmenu(menus, 0, @in_sc_openscedlg, '&Import Data... ','I');
in_addmenu(menus, 0, @in_closeRequest, '&Close','W');
in_addmenu(menus, 1, {@gui.i_savemainfig, 3}, 'Save Figure to PowerPoint File...');
in_addmenu(menus, 0, {@gui.i_savemainfig, 2}, 'Save Figure as Graphic File...');
in_addmenu(menus, 0, {@gui.i_savemainfig, 1}, 'Save Figure as SVG File...');
in_addmenu(menus, 1, @gui.callback_SaveX, 'Export && &Save Data...', 'S');
case 2
menus = uimenu(FigureHandle, 'Text', '&Edit');
in_addmenu(menus, 0, @in_SelectCellsByQC, 'Filter Genes & Cells...', 'F');
in_addmenu(menus, 1, @in_Brushed2NewCluster, 'Add Brushed Cells to a New Group');
in_addmenu(menus, 0, @in_Brushed2MergeClusters, 'Merge Brushed Cells to Same Group');
in_addmenu(menus, 0, @in_RenameCellTypeBatchID, 'Rename Cell Type or Batch ID...');
in_addmenu(menus, 1, @gui.callback_SplitAtacGex, 'Split Multiome ATAC+GEX Matrix...');
in_addmenu(menus, 1, {@in_MergeSCEs, 1}, 'Merge SCE Data Variables in Workspace...');
in_addmenu(menus, 0, {@in_MergeSCEs, 2}, 'Merge SCE Data Files...');
in_addmenu(menus, 1, @in_AddEditCellAttribs, 'Add/Edit Cell Attributes...');
in_addmenu(menus, 0, @in_ExportCellAttribTable, 'Export Cell Attribute Table...');
in_addmenu(menus, 1, @gui.callback_SelectCellsByMarker, 'Extract Cells by Marker (+/-) Expression...');
in_addmenu(menus, 0, @in_MergeSubCellTypes, 'Merge Subclusters of Same Cell Type');
in_addmenu(menus, 1, {@in_WorkonSelectedGenes, 'name'}, 'Select Genes to Work on...');
in_addmenu(menus, 0, {@in_WorkonSelectedGenes, 'hvg'}, 'Select Highly Variable Genes (HVGs) to Work on...');
in_addmenu(menus, 0, {@in_WorkonSelectedGenes, 'ligandreceptor'}, 'Select Ligand Receptor Genes to Work on...');
in_addmenu(menus, 0, @in_SubsampleCells, 'Subsample 50% Cells to Work on...');
in_addmenu(menus, 1, {@in_DeleteBrushedOrUnbrushedCells, 'brushed'}, 'Delete Brushed Cells...');
in_addmenu(menus, 0, {@in_DeleteBrushedOrUnbrushedCells, 'unbrushed'}, 'Delete Unbrushed Cells...');
in_addmenu(menus, 1, @gui.callback_SelectCellsByClass, 'Select Cells by Class & Open in New Window...');
case 3
menus = uimenu(FigureHandle, 'Text', '&View');
in_addmenu(menus, 0, @in_EmbeddingAgain, 'Embed Cells Using tSNE, UMP, PHATE...', 'B');
in_addmenu(menus, 0, @in_Switch2D3D, 'Switch Between 2D/3D Embeddings...');
in_addmenu(menus, 1, @in_ClusterCellsS, "Cluster Cells Using Cell Embedding (S)", 'C');
in_addmenu(menus, 0, @in_ClusterCellsX, "Cluster Cells Using Expression Matrix (X) 🐢 ...");
in_addmenu(menus, 1, @gui.callback_ShowGeneExpr, 'Gene Expression...', 'E');
in_addmenu(menus, 0, @in_ShowCellStates, 'Show Cell States...', 'T');
in_addmenu(menus, 0, @in_labelcellgroups, 'Label Cell Groups...', 'G');
in_addmenu(menus, 0, @in_highlightcellgroups, 'Highlight Cell Groups...');
in_addmenu(menus, 0, @gui.callback_MultiGroupingView, 'Multi-Grouping View...');
in_addmenu(menus, 0, @gui.callback_CrossTabulation, 'Cross Tabulation');
in_addmenu(menus, 0, @gui.callback_ShowGeneExprGroup, 'Gene Expression in Groups');
in_addmenu(menus, 1, @gui.callback_ViewMetaData, 'View Metadata...', 'M');
in_addmenu(menus, 1, @gui.callback_ShowHgBGeneExpression, 'Hemoglobin (Hgb) Genes Expression...');
in_addmenu(menus, 0, @gui.callback_ShowMtGeneExpression, 'Mitochondrial (Mt-) Genes Expression...');
in_addmenu(menus, 0, @in_qcviolin, 'Cell QC Metrics in Violin Plots...');
in_addmenu(menus, 1, @gui.callback_ShowClustersPop,"Show Cell Clusters/Groups Individually...");
in_addmenu(menus, 1, @gui.callback_CloseAllOthers, 'Close All Other Figures', 'X');
in_addmenu(menus, 0, @in_RefreshAll, 'Refresh Current View', 'R');
case 4
menus = uimenu(FigureHandle, 'Text', '&Plots');
in_addmenu(menus, 0, @gui.callback_Dotplot, 'Gene Expression Dot Plot...');
in_addmenu(menus, 0, @gui.callback_Heatmap, 'Gene Expression Heatmap...');
in_addmenu(menus, 0, @gui.callback_ScatterStemPlot,'Gene Expression/Cell State Stem Plot...');
in_addmenu(menus, 0, @gui.callback_Violinplot, 'Gene Expression/Cell State Violin Plot...');
in_addmenu(menus, 0, @gui.callback_ScatterCorrPlot,'Correlation Plot...');
in_addmenu(menus, 1, @gui.callback_ShowGeneExprCompr,'Side-by-Side Gene Expression...');
in_addmenu(menus, 0, @gui.callback_EnrichrTab2Circos,'Enrichr Result Table to Circos Plot...');
in_addmenu(menus, 1, @gui.callback_GetCellSignatureMatrix, 'Cell State Radar Plot...');
in_addmenu(menus, 0, @in_DrawKNNNetwork, 'Cell kNN Network...');
in_addmenu(menus, 0, @in_DrawTrajectory, 'Cell Trajectory...');
in_addmenu(menus, 1, @gui.callback_PickPlotMarker,'Next Marker Type');
in_addmenu(menus, 0 ,@gui.callback_PickColorMap,'Next Colormap');
in_addmenu(menus, 1 ,@in_cleanumap,'Clean tSNE/UMAP/PHATE Plot');
case 5
menus = uimenu(FigureHandle, 'Text', 'Anno&tate');
in_addmenu(menus, 0, {@in_DetermineCellTypeClustersGeneral, true}, "Annotate Cell Types Using PanglaoDB Marker Genes");
in_addmenu(menus, 0, {@in_DetermineCellTypeClustersGeneral, false}, 'Annotate Cell Types Using Customized Marker Genes...');
in_addmenu(menus, 1, {@in_MergeCellSubtypes, 1}, 'Import Cell Annotation from SCE in Workspace...');
in_addmenu(menus, 0, {@in_MergeCellSubtypes, 2}, 'Import Cell Annotation from SCE Data File...');
in_addmenu(menus, 1, @in_Brush4Celltypes, "Annotate Cell Types for Brushed Cells");
in_addmenu(menus, 0, @gui.callback_Brush4Markers, "Find Marker Genes for Brushed Cells");
in_addmenu(menus, 0, @gui.callback_FindAllMarkers, "Make Marker Gene Heatmap");
in_addmenu(menus, 1, {@in_CellCyclePotency, 1}, 'Estimate Cell Cycle Phase...');
in_addmenu(menus, 0, {@in_CellCyclePotency, 2}, 'Estimate Differentiation Potency...');
in_addmenu(menus, 0, {@in_CellCyclePotency, 3}, 'Estimate Stemness...');
in_addmenu(menus, 0, {@in_CellCyclePotency, 4}, 'Estimate Dissociation Gene Ratio...');
in_addmenu(menus, 1, @in_SingleClickSolution, 'Single Click Solution (from Raw Data to Annotation)...');
case 6
menus = uimenu(FigureHandle, 'Text', '&Analyze');
in_addmenu(menus, 0, @gui.callback_CalculateGeneStats, 'Gene Expression (Statistics) Analysis...');
in_addmenu(menus, 0, @in_EnrichrHVGs, 'Gene Variability (HVG Function) Analysis...');
in_addmenu(menus, 0, @in_CompareCellScoreBtwCls, 'Gene Program (Cell Score) Analysis...');
in_addmenu(menus, 1, @gui.callback_DEGene2Groups, 'Differential Expression (DE) Analysis...','D');
in_addmenu(menus, 0, @gui.callback_DVGene2Groups, 'Differential Variability (DV) Analysis...','V');
in_addmenu(menus, 0, @gui.callback_DPGene2Groups, 'Differential Program (DP) Analysis...','P');
in_addmenu(menus, 1, @gui.callback_DEGene2GroupsBatch, 'DE Analysis in Cell Type Batch Mode...');
in_addmenu(menus, 0, @gui.callback_DVGene2GroupsBatch, 'DV Analysis in Cell Type Batch Mode...');
in_addmenu(menus, 0, @gui.callback_DPGene2GroupsBatch, 'DP Analysis in Cell Type Batch Mode...');
in_addmenu(menus, 1, @gui.callback_DEVP2GroupsBatch, 'All (DE, DV, DP) Analysis in Cell Type Batch Mode...');
in_addmenu(menus, 1, @gui.callback_RunEnrichr, 'Enrichr Analysis...');
case 7
menus = uimenu(FigureHandle, 'Text', '&Network');
in_addmenu(menus, 0, @in_Select5000Genes, 'Remove Less Informative Genes to Reduce Gene Space...');
in_addmenu(menus, 0, @gui.callback_DrawNetwork, 'Plot GRN from Edge (Gene Pair) List...');
in_addmenu(menus, 1, @gui.callback_BuildGeneNetwork, 'Build GRN with Selected Genes...');
in_addmenu(menus, 0, @gui.callback_CompareGeneNetwork, 'Build & Compare GRNs...');
in_addmenu(menus, 1, {@in_scTenifoldNet,1}, 'Construct GRN with All Genes - scTenifoldNet [PMID:33336197] 🐢...');
in_addmenu(menus, 0, {@in_scTenifoldNet,2}, 'Construct & Compare GRNs - scTenifoldNet [PMID:33336197] 🐢...');
in_addmenu(menus, 1, @gui.callback_scTenifoldKnk1, 'Virtual Gene Knockout - scTenifoldKnk [PMID:35510185] 🐢 ...');
in_addmenu(menus, 0, @gui.callback_VirtualKOGenKI, 'Virtual Gene Knockout (GenKI/🐍) [PMID:37246643] ...');
%in_addmenu(menus, 0, @gui.callback_VirtualKOGenKI, 'Virtual Gene Knockout (GenKI/🐍) [PMID:37246643] 🐢 ...');
%in_addmenu(menus, 1, @gui.callback_scTenifoldXct, 'Cell-Cell Communication (scTenifoldXct/🐍) [PMID:36787742] 🐢 ...');
in_addmenu(menus, 1, @gui.callback_scTenifoldXct, 'One-Sample Cell-Cell Communication (scTenifoldXct/🐍) [PMID:36787742]...');
in_addmenu(menus, 0, @gui.callback_scTenifoldXct2, 'Two-Sample Cell-Cell Communication (scTenifoldXct2/🐍) [PMID:36787742]...');
in_addmenu(menus, 0, @gui.callback_scTenifoldCko, 'Virtual Cell-Cell Communication Knockout - scTenifoldCko/🐍 [Experimental] 🐢 ...');
case 8
menus = uimenu(FigureHandle, 'Text', 'E&xternal');
in_addmenu(menus, 0, @gui.i_resetrngseed, 'Set Random Seed...');
in_addmenu(menus, 0, @gui.i_setextwd, 'Set Working Folder...');
in_addmenu(menus, 1, @gui.i_setscimilaritymodelpath, 'Set Scimilarity Model...');
in_addmenu(menus, 0, @gui.i_setllmmodel, 'Set Large Language Model...');
in_addmenu(menus, 1, @gui.i_setrenv, 'Set Up R (ℝ) Environment');
in_addmenu(menus, 0, @gui.i_setpyenv, 'Set Up Python (🐍) Environment');
in_addmenu(menus, 1, @in_RunSeuratWorkflow, 'ℝ - Run Seurat Workflow (Seurat) [PMID:25867923]...');
in_addmenu(menus, 0, @in_RunMonocle3, 'ℝ - Pseudotime Analysis (Monocle3) [PMID:28825705]...');
in_addmenu(menus, 0, {@in_CellCyclePotency, 5}, 'ℝ - Aneuploid/Diploid Analysis (copykat) [PMID:33462507]...');
in_addmenu(menus, 0, @in_DecontX, 'ℝ - Detect Ambient RNA Contamination (DecontX) [PMID:32138770]...');
in_addmenu(menus, 1, @in_RunDataMapPlot, '🐍 - Run DataMapPlot (datamapplot)...');
in_addmenu(menus, 0, @in_DoubletDetection, '🐍 - Detect Doublets (Scrublet) [PMID:30954476]...');
in_addmenu(menus, 0, @in_HarmonyPy, '🐍 - Batch Integration (Harmony) [PMID:31740819]...');
in_addmenu(menus, 0, @in_SCimilarity, '🐍 - Annotate Cell Types (Scimilarity) [PMID:39566551]...');
in_addmenu(menus, 0, {@in_SubsampleCells, 2}, '🐍 - Geometric Sketching (geosketch) [PMID:31176620]...');
in_addmenu(menus, 0, @gui.callback_MELDPerturbationScore, '🐍 - MELD Perturbation Score (MELD) [PMID:33558698]...');
% in_addmenu(menus, 1, @gui.callback_ExploreCellularCrosstalk, 'Talklr Intercellular Crosstalk [DOI:10.1101/2020.02.01.930602]...');
case 9
%menus = uimenu(FigureHandle, 'Text', '&Options');
%in_addmenu(menus, 0, @gui.i_resetrngseed, 'Set Random Seed...');
%in_addmenu(menus, 0, @gui.i_setextwd, 'Set Working Folder...');
%in_addmenu(menus, 1, @gui.i_setllmmodel, 'Set LLM Provider && Model...');
case 10
menus = uimenu(FigureHandle, 'Text', '&Help');
in_addmenu(menus, 0, {@(~, ~) web('https://scgeatoolbox.readthedocs.io/en/latest/')}, 'Online Documentation...');
in_addmenu(menus, 0, {@(~, ~) gui.gui_uishowrefinfo('Quick Installation',FigureHandle)}, 'Quick Installation Guide...');
in_addmenu(menus, 0, {@(~, ~) gui.gui_uishowrefinfo('Shortcuts Guide',FigureHandle)}, 'Shortcuts User Guide...');
in_addmenu(menus, 1, {@(~, ~) web('https://www.mathworks.com/matlabcentral/fileexchange/72917-scgeatoolbox-single-cell-gene-expression-analysis-toolbox')}, 'View scGEAToolbox on File Exchange...');
in_addmenu(menus, 0, {@(~, ~) web('https://pubmed.ncbi.nlm.nih.gov/31697351/')}, 'Cite scGEAToolbox Paper...');
in_addmenu(menus, 0, {@(~, ~) web('https://scholar.google.com/scholar?cites=4661048952867744439&as_sdt=5,44&sciodt=0,44&hl=en')}, 'Papers Citing scGEAToolbox...');
in_addmenu(menus, 1, {@(~, ~) web('https://scgeatool.github.io/')}, 'Visit SCGEATOOL-Standalone Website...');
in_addmenu(menus, 0, {@(~, ~) web('https://matlab.mathworks.com/open/github/v1?repo=jamesjcai/scGEAToolbox&file=online_landing.m')}, 'Run SCGEATOOL in MATLAB Online...');
in_addmenu(menus, 1, @gui.callback_CheckUpdates, 'Check for Updates...');
[~, ~, ~, im] = i_majvercheck([false false false true]);
in_addmenu(menus, 1, {@(~, ~) gui.sc_simpleabout(FigureHandle, im)}, 'About SCGEATOOL');
end
end
function createPushButtons(FigureHandle)
in_addbuttonpush(0, 0, [], [], "");
in_addbuttonpush(0, 0, @gui.callback_MultiGroupingView, "visibility_18dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Multi-grouping View...");
in_addbuttonpush(0, 0, @gui.callback_CrossTabulation, "full_stacked_bar_chart_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Cross tabulation");
in_addbuttonpush(0, 0, @gui.callback_ShowGeneExprGroup, "dataset_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Gene expression in groups");
in_addbuttonpush(0, 1, @gui.callback_Dotplot, "icon-mat-blur-linear-10.gif", "Gene Expression Dot Plot...");
in_addbuttonpush(0, 0, @gui.callback_Heatmap, "icon-mat-apps-20.gif", "Gene Expression Heatmap...");
in_addbuttonpush(0, 0, @gui.callback_ScatterStemPlot, "signal_cellular_pause_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Gene Expression/Cell State Stem Plot...");
in_addbuttonpush(0, 0, @gui.callback_Violinplot, "violinplot.gif", "Gene Expression/Cell State Violin Plot...");
in_addbuttonpush(0, 0, @gui.callback_ScatterCorrPlot, "icon-mat-blur-off-10a.gif", "Correlation Plot...");
in_addbuttonpush(0, 0, [], [], "");
in_addbuttonpush(0, 1, @in_CompareCellScoreBtwCls, "barcode_scanner_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Cell score analysis--obtaining gene signature score for each cell");
in_addbuttonpush(0, 0, @gui.callback_GetCellSignatureMatrix, "hexagon_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Cell state analysis--obtaining multiple gene signature scores to reveal functional state of cells");
in_addbuttonpush(0, 1, @gui.callback_DEGene2Groups, "graphic_eq_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Differential expression (DE) analysis");
in_addbuttonpush(0, 0, @gui.callback_DVGene2Groups, "edit_audio_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Differential variability (DV) analysis");
in_addbuttonpush(0, 0, @gui.callback_DPGene2Groups, "data_exploration_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Differential program (DP) analysis");
in_addbuttonpush(0, 0, [], [], "");
in_addbuttonpush(0, 1, @gui.callback_BuildGeneNetwork, "graph_3_18dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Build gene regulatory network");
in_addbuttonpush(0, 0, @gui.callback_CompareGeneNetwork, "graph_5_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Compare two scGRNs");
in_addbuttonpush(0, 1, {@gui.i_savemainfig, 3}, "presentation.jpg", 'Save Figure to PowerPoint File...');
gui.gui_3dcamera(DeftToolbarHandle);
pt = uitoggletool(DeftToolbarHandle);
try
load(fullfile(mfolder, 'resources', 'Images', 'colorbarcdata.mat'), 'CData');
pt.CData = CData;
catch
pt.CData = rand(16, 16, 3);
end
pt.Tooltip = 'Insert Colorbar';
pt.ClickedCallback = @in_addcolorbar;
pt.Tag = "figToglColorbar";
in_addbuttonpush(0, 0, @gui.callback_CloseAllOthers, "xmark-square.jpg", "Close all other figures");
in_addbuttonpush(0, 0, {@gui.i_resizewin, FigureHandle}, 'scale-frame-reduce.jpg', 'Resize Plot Window')
in_addbuttontoggle(1, 0, {@in_togglebtfun, @in_turnoffuserguiding, "icon-mat-unfold-more-10.gif", "icon-mat-unfold-less-10.gif", false, "Turn on/off user onboarding toolbar"});
in_addbuttonpush(1, 0, @gui.callback_ShowGeneExpr, "google-docs.jpg", "Select genes to show expression")
in_addbuttonpush(1, 0, @in_ShowCellStates, "bookmark-book.jpg", "Show cell states")
in_addbuttonpush(1, 0, @in_SelectCellsByQC, "filter-alt.jpg", "Filter genes & cells")
in_addbuttonpush(1, 1, @in_labelcellgroups, "label.jpg", "Label cell groups");
in_addbuttonpush(1, 0, @in_Brushed2NewCluster, "substract.jpg", "Add brushed cells to a new group")
in_addbuttonpush(1, 0, @in_Brushed2MergeClusters, "union.jpg", "Merge brushed cells to same group")
in_addbuttonpush(1, 0, @in_RenameCellTypeBatchID, "edit.jpg", "Rename cell type or batch ID");
in_addbuttonpush(1, 0, @in_SingleClickSolution, "apple-swift.jpg", "Single-click cell type annotation")
in_addbuttonpush(1, 0, [], [], "");
in_addbuttonpush(1, 1, @in_ClusterCellsS, "bubble_chart_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Clustering using cell embedding (S)")
in_addbuttonpush(1, 0, {@in_DetermineCellTypeClustersGeneral, true}, "auto_transmission_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Assign cell types to groups")
in_addbuttonpush(1, 0, @in_Brush4Celltypes, "color-picker.jpg", "Assign cell type to selected cells");
in_addbuttonpush(1, 1, @gui.callback_Brush4Markers, "medal1st.jpg", "Marker genes of brushed cells");
in_addbuttonpush(1, 0, @gui.callback_FindAllMarkers, "grain_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Marker gene heatmap");
in_addbuttonpush(1, 0, [], [], "");
in_addbuttonpush(1, 1, @gui.callback_ShowClustersPop, "view-grid.jpg", "Show cell clusters/groups individually");
in_addbuttonpush(1, 0, @gui.callback_SelectCellsByClass, "checklist_rtl_18dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Select cells by class/group & open in new window");
in_addbuttonpush(1, 0, @in_DeleteSelectedCells, "variable_remove_18dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Delete brushed/selected cells");
in_addbuttonpush(1, 0, @gui.callback_SaveX, "floppy-disk.jpg", "Export & save data");
in_addbuttonpush(1, 1, @in_EmbeddingAgain, "cinema-old.jpg", "Embedding (tSNE, UMP, PHATE)");
in_addbuttonpush(1, 0, @in_Switch2D3D, "perspective-view.jpg", "Switch 2D/3D");
in_addbuttonpush(1, 0, @gui.callback_PickPlotMarker, "palette.jpg", "Switch scatter plot marker type");
in_addbuttonpush(1, 0, @gui.callback_PickColorMap, "color-wheel.jpg", "Pick new color map");
in_addbuttonpush(1, 0, @in_RefreshAll, "refresh_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", "Refresh");
in_addbuttonpush(2, 0, @in_turnonuserguiding, "icon-fa-thumb-tack-10.gif", "Turn on user guiding toolbar");
in_addbuttontoggle(2, 0, {@in_togglebtfun, @in_SelectCellsByQC, "icon-mat-filter-1-10.gif", "filter-alt.jpg", true, "Filter genes & cells"});
in_addbuttontoggle(2, 0, {@in_togglebtfun, @in_EmbeddingAgain, "icon-mat-filter-2-10.gif", "cinema-old.jpg", true, "Embedding (tSNE, UMP, PHATE)"});
in_addbuttontoggle(2, 0, {@in_togglebtfun, @in_ClusterCellsS, "icon-mat-filter-3-10.gif", "bubble_chart_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", true, "Clustering using embedding S"});
in_addbuttontoggle(2, 0, {@in_togglebtfun, @in_DetermineCellTypeClustersGeneral, "icon-mat-filter-4-10.gif", "auto_transmission_16dp_000000_FILL0_wght400_GRAD0_opsz20.jpg", true, "Assign cell types to groups"});
in_addbuttontoggle(2, 0, {@in_togglebtfun, @gui.callback_SaveX, "icon-mat-filter-5-10.gif", "floppy-disk.jpg", true, "Export & save data"});
end
function in_sc_openscedlg(~, event)
if strcmp(event.EventName,'KeyPress') && ~ismember(event.Key,{'return','space','i','I'}), return; end
clickType = get(FigureHandle, 'SelectionType');
if strcmp(clickType,'alt'), return; end
set(button1,'Enable','off');
if ~isempty(sce) && sce.NumCells > 0
if ~strcmp(questdlg('Current SCE will be replaced. Continue?',''),'Yes')
set(button1,'Enable','on');
return;
end
end
[sce, filename] = gui.sc_openscedlg;
if ~isempty(sce) && sce.NumCells > 0 && sce.NumGenes > 0
guidata(FigureHandle, sce);
c=[];
in_RefreshAll([], [], false, false);
else
set(button1,'Enable','on');
uicontrol(button1);
if ~isempty(sce)
uiwait(warndlg('Imported SCE contains no cells.',''));
end
end
sprintf('Read data from %s.\n', filename);
try
[~, ~, ext] = fileparts(filename);
if strcmp(ext, '.h5ad')
% if strcmp('.h5ad', extractAfter(filename, strlength(filename)-5))
switch questdlg('Read more cell info, e.g., cell type or batch id (if any) from .h5ad file')
case 'Yes'
[sce] = gui.gui_readh5adinfo(filename, sce);
end
end
catch
end
end
function in_fixfield(oldf, newf)
if ~isfield(sce.struct_cell_embeddings,newf) && isfield(sce.struct_cell_embeddings,oldf)
if ~isempty(sce.struct_cell_embeddings.(oldf))
if size(sce.struct_cell_embeddings.(oldf),2) == 3
sce.struct_cell_embeddings.(newf) = sce.struct_cell_embeddings.(oldf);
sce.struct_cell_embeddings = rmfield(sce.struct_cell_embeddings,oldf);
end
end
end
if isfield(sce.struct_cell_embeddings, oldf)
if isempty(sce.struct_cell_embeddings.(oldf))
sce.struct_cell_embeddings = rmfield(sce.struct_cell_embeddings,oldf);
end
end
end
function in_cleanumap(~, ~)
answer = questdlg('Select embedding method label.', ...
'','tSNE','UMAP','PHATE','tSNE');
if isempty(answer), return; end
a = colormap;
gui.i_baredrplot(hAx, [], answer, FigureHandle);
colormap(a);
end
function in_CompareCellScoreBtwCls(src, events)
if gui.callback_CompareCellScoreBtwCls(src, events)
sce = guidata(FigureHandle);
end
end
function in_CellCyclePotency(src, events, typeid)
if gui.callback_CellCyclePotency(src, events, typeid)
sce = guidata(FigureHandle);
end
end
function in_RunMonocle3(src, events)
if gui.callback_RunMonocle3(src, events)
sce = guidata(FigureHandle);
[y, idx] = ismember({'monocle3_pseudotime'}, ...
sce.list_cell_attributes(1:2:end));
if y
answer = questdlg('Color cells using pseudotime T and show Monocle3 embedding S?',...
'','Yes','Color cells only','Show embedding only','Yes');
switch answer
case 'Yes'
sce.c = sce.list_cell_attributes{idx*2};
sce.s = sce.struct_cell_embeddings.('monocle2d');
[c, cL] = grp2idx(sce.c);
in_RefreshAll(src, [], true, false);
case 'Color cells only'
sce.c = sce.list_cell_attributes(idx*2);
[c, cL] = grp2idx(sce.c);
in_RefreshAll(src, [], true, false);
case 'Show embedding only'
sce.s = sce.struct_cell_embeddings.('monocle2d');
in_RefreshAll(src, [], true, false);
otherwise
end
end
end
end
function in_turnonuserguiding(~, ~)
% setpref('scgeatoolbox','useronboardingtoolbar',true);
% set(UserToolbarHandle, 'Visible', 'on');
Button = gui.gui_userguidingpref(false);
switch Button
case 'Yes'
case 'No'
in_turnoffuserguiding;
case 'Cancel'
end
end
function in_turnoffuserguiding(~, ~)
if get(UserToolbarHandle, 'Visible') == "off"
askpref = true;
else
askpref = false;
end
if showuseronboarding
set(UserToolbarHandle, 'Visible', 'off');
else
set(UserToolbarHandle, 'Visible', 'on');
end
showuseronboarding = ~showuseronboarding;
if askpref
% gui.gui_userguidingpref(false);
%answer=questdlg('Show User Onboarding Toolbar again next time?','');
%switch answer
% case 'Yes'
% setpref('scgeatoolbox','useronboardingtoolbar',true);
% case 'No'
% setpref('scgeatoolbox','useronboardingtoolbar',false);
%end
end
end
function in_addmenu(menuHdl, sepTag, callbackFnc, tooltipTxt, acchar)
if nargin<5, acchar=''; end
if ischar(callbackFnc) || isstring(callbackFnc)
callbackFnc = str2func(callbackFnc);
end
if sepTag == 1
septag = 'on';
else
septag = 'off';
end
uimenu(menuHdl, 'Text', tooltipTxt, ...
'Separator', septag, ...
'Callback', callbackFnc, ...
'Accelerator', acchar, ...
'Tag', "figMenu" + matlab.lang.makeValidName(tooltipTxt));
end
function in_addbuttonpush(toolbarHdl, sepTag, callbackFnc, imgFil, tooltipTxt)
if ischar(callbackFnc) || isstring(callbackFnc)
callbackFnc = str2func(callbackFnc);
end
if toolbarHdl == 0
barhandle = DeftToolbarHandle;
elseif toolbarHdl == 1
barhandle = MainToolbarHandle;
elseif toolbarHdl == 2
barhandle = UserToolbarHandle;
end
if numel(ptImgCell) >= ptimgidx && ~isempty(ptImgCell{1, ptimgidx})
pkg.i_addbutton2fig(barhandle, sepTag, ...
callbackFnc, ptImgCell{1, ptimgidx}, tooltipTxt);
else
[~, ptImgCell{1, ptimgidx}] = pkg.i_addbutton2fig(barhandle, ...
sepTag, callbackFnc, imgFil, tooltipTxt);
ptImgCell{2, ptimgidx} = tooltipTxt;
end
ptimgidx = ptimgidx + 1;
end
function in_addbuttontoggle(toolbarHdl, sepTag, callbackFnc)
imgFil = callbackFnc{3};
tooltipTxt = callbackFnc{6};
%if ischar(callbackFnc{1}) || isstring(callbackFnc{1})
% callbackFnc=str2func(callbackFnc{1});
%end
if toolbarHdl == 0
barhandle = DeftToolbarHandle;
elseif toolbarHdl == 1
barhandle = MainToolbarHandle;
elseif toolbarHdl == 2
barhandle = UserToolbarHandle;
end
pt = uitoggletool(barhandle, 'Separator', sepTag);
pt.CData = in_getPtImage(imgFil);
pt.Tooltip = tooltipTxt;
pt.ClickedCallback = callbackFnc;
%callbackFnc =
% 1×6 cell array
% {function_handle} {function_handle} {["icon-mat-filt…"]} {["plotpicker-co…"]} {[1]} {["Assign cell t…"]}
%pt.Tag = "figTogl" + matlab.lang.makeValidName(tooltipTxt);
end
function in_togglebtfun(src, ~, func, ~, imgFil, ...
actiondelay, tooltipTxt)
if nargin < 6, actiondelay = true; end
src.CData = in_getPtImage(imgFil);
if actiondelay
if src.State == "off"
func(src);
else
s = 'To execute the function, click the button again or locate and click the same button in the toolbar above. Hover over the button to view a description of its function.';
try
uiwait(helpdlg(sprintf('%s\n%s', upper(tooltipTxt), s), ''));
catch
end
end
else
func(src);
end
end
function [ptImage] = in_getPtImage(imgFil)
try
[ptImage, map] = imread(fullfile(mfolder, 'resources', 'Images', imgFil));
catch
try
[ptImage, map] = imread(fullfile(matlabroot,'toolbox', ...
'matlab','icons', imgFil));
catch
map = [];
ptImage = rand(16, 16, 3);
end
end
if ~isempty(map), ptImage = ind2rgb(ptImage, map); end
if size(ptImage, 3) == 1, ptImage = cat(3, ptImage, ptImage, ptImage); end
end
% ------------------------
% Callback Functions
% ------------------------
function in_addcolorbar(~,~)
cbtogg = findall(FigureHandle, 'Tag', 'figToglColorbar');
if ~isempty(cbtogg) && isequal(cbtogg,gcbo) && strcmpi(get(cbtogg,'State'),'on')
colorbar(hAx);
else
colorbar(hAx,'off')
end
end
function in_closeRequest(hObject, ~)
if ~(ismcc || isdeployed)
if isempty(sce) || sce.NumCells==0
ButtonName = 'no';
else
ButtonName = questdlg('Save SCE before closing SCGEATOOL?');
end
switch lower(ButtonName)
case 'yes'
if ~isempty(callinghandle)
guidata(callinghandle, sce);
delete(hObject);
uiwait(helpdlg('SCE updated.',''));
else
if gui.callback_SaveX(FigureHandle,[])
pause(1);
delete(hObject);
end
end
case 'cancel'
return;
case 'no'
delete(FigureHandle);
otherwise
return;
end
else
delete(hObject);
end
end
function in_qcviolin(~, ~)
gui.i_qcviolin(sce.X, sce.g, FigureHandle);
end
function in_RunDataMapPlot(src, ~)
if ~pkg.i_checkpython
uiwait(warndlg('Python is not installed.',''));
return;
end
ndim = 2;
[vslist] = gui.i_checkexistingembed(sce, ndim);
if isempty(h.ZData) && size(sce.s,2)==2 && length(vslist) <= 1
gui.callback_RunDataMapPlot(src, []);
elseif isempty(h.ZData) && size(sce.s,2)==2 && length(vslist) > 1
switch questdlg('Using current 2D embedding?')
case 'Yes'
gui.callback_RunDataMapPlot(src, []);
case 'No'
[sx] = gui.i_pickembedvalues(sce, 2);
if ~isempty(sx) && size(sx,1) == sce.NumCells
sce.s = sx;
else
warning('Running error.');
return;
end
guidata(FigureHandle, sce);
gui.callback_RunDataMapPlot(src, []);
case 'Cancel'
return;
end
elseif ~isempty(h.ZData)
if strcmp(questdlg('This function requires 2D embedding. Continue?'), 'Yes'), in_Switch2D3D(src,[]); end
end
end
function in_SubtypeAnnotation(src, ~)
[requirerefresh] = gui.callback_SubtypeAnnotation(src, []);
if requirerefresh
sce = guidata(FigureHandle);
[c, cL] = grp2idx(sce.c_cell_type_tx);
in_RefreshAll(src, [], true, false);
ix_labelclusters(true);
end
end
function in_MergeCellSubtypes(src, ~, sourcetag, allcell)
if nargin < 4
switch questdlg('Import annotation for all cells or just cells of a subtype?', '', ...
'All Cells', 'Subtype Cells', 'Cancel', 'All Cells')
case 'All Cells'
allcell = true;
case 'Subtype Cells'
allcell = false;
case 'Cancel'
return;
otherwise
return;
end
end
[requirerefresh] = gui.callback_MergeCellSubtypes(src, [], sourcetag, allcell);
if requirerefresh
sce = guidata(FigureHandle);
[c, cL] = grp2idx(sce.c_cell_type_tx);
in_RefreshAll(src, [], true, false);
ix_labelclusters(true);
end
end
function in_MergeSCEs(src, ~, sourcetag)
[requirerefresh, s] = gui.callback_MergeSCEs(src, sourcetag);
if requirerefresh && ~isempty(s)
sce = guidata(FigureHandle);
[c, cL] = grp2idx(sce.c_batch_id);
sce.c = c;
if sce.NumCells==0
uiwait(warndlg('Merged SCE contains no cells.',''));
return;
else
in_RefreshAll(src, [], true, false);
uiwait(helpdlg(sprintf('%s SCEs merged.', upper(s)), ''));
end
end
end
function in_WorkonSelectedGenes(src, ~, type)
if nargin < 1, type = 'name'; end
switch type
case 'name'
[glist] = gui.i_selectngenes(sce, [], FigureHandle);
if isempty(glist), return; end
[y, idx] = ismember(glist, sce.g);
if ~all(y)
errordlg('Runtime error.','');
return;
end
case 'hvg'
k = gui.i_inputnumk(2000, 1, sce.NumGenes, 'the number of HVGs');
if isempty(k), return; end
answer = questdlg('Which HVG detecting method to use?', '', ...
'Splinefit Method [PMID:31697351]', ...
'Brennecke et al. (2013) [PMID:24056876]', ...
'Splinefit Method [PMID:31697351]');
switch answer
case 'Brennecke et al. (2013) [PMID:24056876]'
fw = gui.gui_waitbar;
T = sc_hvg(sce.X, sce.g);
case 'Splinefit Method [PMID:31697351]'
fw = gui.gui_waitbar;
T = sc_splinefit(sce.X, sce.g);
otherwise
return;
end
glist = T.genes(1:min([k, sce.NumGenes]));
[y, idx] = ismember(glist, sce.g);
if ~all(y)
errordlg('Runtime error.','');
return;
end
case 'ligandreceptor'
fw = gui.gui_waitbar;
load(fullfile(mfolder, 'resources', 'Ligand_Receptor', ...
'Ligand_Receptor_more.mat'), 'ligand','receptor');
idx = ismember(upper(sce.g), unique([ligand; receptor]));
if ~any(idx)
errordlg('Runtime error: No gene left after selection.','');
return;
end
if sum(idx) < 50
if ~strcmp(questdlg('Few genes (n < 50) selected. Continue?',''), 'Yes'), return; end
end
end
sce.g = sce.g(idx);
sce.X = sce.X(idx, :);
gui.gui_waitbar(fw);
guidata(FigureHandle, sce);
in_RefreshAll(src, [], true, false);
end
function in_SubsampleCells(src, ~, methodoption)
if nargin < 3, methodoption = []; end
if ~strcmp(questdlg('This function subsamples 50% of cells. Continue?',''), 'Yes'), return; end
if isempty(methodoption)
answer = questdlg('Select method:', '', ...
'Uniform Sampling', ...
'Geometric Sketching [PMID:31176620]', 'Uniform Sampling');
switch answer
case 'Uniform Sampling'
methodoption = 1;
case 'Geometric Sketching [PMID:31176620]'
if ~pkg.i_checkpython
uiwait(warndlg('Python not installed.',''));
return;
end
methodoption = 2;
otherwise
return;
end
end
tn = round(sce.NumCells/2);
if methodoption == 1
rng("shuffle");
idx = randperm(sce.NumCells);
ids = idx(1:tn);
elseif methodoption == 2
if ~gui.gui_showrefinfo('Geometric Sketching [PMID:31176620]'), return; end
fw = gui.gui_waitbar;
Xn = log1p(sc_norm(sce.X))';
[~, Xn] = pca(Xn, 'NumComponents', 300);
gui.gui_waitbar(fw);
try
ids = run.py_geosketch(Xn, tn);
catch ME
gui.gui_waitbar(fw, true);
errordlg(ME.message,'');
return;
end
end
if ~isempty(ids)
sce = sce.selectcells(ids);
c = sce.c;
in_RefreshAll(src, [], true, false);
guidata(FigureHandle, sce);
else
errordlg('Runtime error. No action is taken.','');
end
end
function in_SingleClickSolution(src, ~)
if ~isprop(sce, 'c_cell_type_tx')
disp('The sce object does not have the property c_cell_type_tx.');
return;
end
if ~all(sce.c_cell_type_tx == "undetermined")
if ~strcmp(questdlg("Your data has been embedded and annotated. Single Click Solution will re-embed and annotate cells. Current embedding and annotation will be overwritten. Continue?", ""), 'Yes'), return; end
else
if ~gui.gui_showrefinfo('Single Click Solution'), return; end
end
%if isempty(speciestag)
speciestag = gui.i_selectspecies(2);
%end
if isempty(speciestag), return; end
prompt = {
'tSNE Embedding?', ...
'Add UMAP Embedding?', ...
'Add PHATE Embedding?', ...
'Estimate Cell Cycles?', ...
'Estimate Differentiation Potency of Cells?'};
dlgtitle = '';
dims = [1, 85];
definput = {'Yes', 'No', 'No', 'Yes', 'No'};
answer = inputdlg(prompt, dlgtitle, dims, definput);
if isempty(answer)
return;
end
fw = gui.gui_waitbar_adv;
gui.gui_waitbar_adv(fw,1/8,'Basic QC Filtering...');
sce = sce.qcfilter;
count = 1;
if ~(strcmpi(answer{count},'Yes') || strcmpi(answer{count},'Y'))
errordlg('tSNE Embedding has to be included.','');
return;
end
count = count + 1;
if strcmpi(answer{count},'Yes') || strcmpi(answer{count},'Y')
gui.gui_waitbar_adv(fw,2/8, 'Embeding Cells Using UMAP...');
sce = sce.embedcells('umap3d', true, true, 3);
end
count = count + 1;
if strcmpi(answer{count},'Yes') || strcmpi(answer{count},'Y')
gui.gui_waitbar_adv(fw,2/8, 'Embeding Cells Using PHATE...');
sce = sce.embedcells('phate3d', true, true, 3);
end
gui.gui_waitbar_adv(fw,2/8, 'Embeding Cells Using tSNE...');
sce = sce.embedcells('tsne3d', true, true, 3);
gui.gui_waitbar_adv(fw,3/8, 'Clustering Cells Using K-means...');
sce = sce.clustercells([], [], true);
gui.gui_waitbar_adv(fw,4/8, 'Annotating Cell Types Using PanglaoDB...');
sce = sce.assigncelltype(speciestag, false);
count = count + 1;
if strcmpi(answer{count},'Yes') || strcmpi(answer{count},'Y')
gui.gui_waitbar_adv(fw,5/8, 'Estimate Cell Cycles...');
sce = sce.estimatecellcycle;
end
count = count + 1;
if strcmpi(answer{count},'Yes') || strcmpi(answer{count},'Y')
gui.gui_waitbar_adv(fw,6/8, 'Estimate Differentiation Potency of Cells...');
sce = sce.estimatepotency(speciestag);
end
gui.gui_waitbar_adv(fw,7/8);
[c,cL] = grp2idx(sce.c_cell_type_tx);
sce.c = c;
gui.gui_waitbar_adv(fw);
in_RefreshAll(src, [], true, false);
ix_labelclusters(true);
%setappdata(FigureHandle, 'cL', cL);
guidata(FigureHandle, sce);
end
function in_SelectCellsByQC(src, ~)
%oldsce = sce;
% oldn = sce.NumCells;
% oldm = sce.NumGenes;
sce.c = c;
guidata(FigureHandle, sce);
try
[requirerefresh, highlightindex] = ...
gui.callback_SelectCellsByQC(src);
catch ME
errordlg(ME.message,'');
return;
end
if requirerefresh
sce = guidata(FigureHandle);
[c, cL] = grp2idx(sce.c);
in_RefreshAll(src, [], true, false);
% newn = sce.NumCells;
% newm = sce.NumGenes;
% answer = questdlg(sprintf('%d cells removed; %d genes removed.', ...
% oldn-newn, oldm-newm),'','Accept Changes', 'Undo Changes', 'Accept Changes');
% if ~strcmp(answer, 'Accept Changes')
% sce = oldsce;
% [c, cL] = grp2idx(sce.c);
% in_RefreshAll(src, [], true, false);
% guidata(FigureHandle, sce);
% end
end
if ~isempty(highlightindex)
h.BrushData = highlightindex;
end
end
function in_Select5000Genes(src, ~)
oldm = sce.NumGenes;
oldn = sce.NumCells;
[requirerefresh, scenew] = gui.callback_Select5000Genes(src);
if requirerefresh