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%This wrapper script runs through the figures and results from the MISS | ||
%manuscript, and regenerates them in order, beginning with the basic | ||
%pipeline results using the AIBS human scRANseq dataset | ||
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%FILEPATH | ||
matdir = '/Users/justintorok/Documents/MATLAB/MISS/Human-related/RawDataFiles'; %define directory to draw from and save data to | ||
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%LOADING INITIAL INPUT DATA | ||
load([matdir filesep 'AIBS_Human_scRNAseq_datastruct_subclass.mat'],'subclass_struct'); | ||
load([matdir filesep 'abagen426_1mm_datastruct.mat'],'regexpr_struct'); | ||
genevct = subclass_struct.averages.genevct; | ||
classkey = subclass_struct.cell_types; | ||
gene_names = subclass_struct.gene_names; | ||
regvgene = regexpr_struct.regvgene; | ||
regvgene_sums = sum(regvgene); | ||
regvgene_sums = repmat(regvgene_sums,size(regvgene,1),1); | ||
regvgene = regvgene ./ regvgene_sums; | ||
clear regexpr_struct subclass_struct | ||
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%MRx3 GENE RANKING USING scRNAseq FROM AIBS | ||
lambda = 90; %percentile of genes to exclude from MRx3 ranking based on projection error added | ||
geneinds = MRx3_Selector_Prefilter(genevct,regvgene,size(regvgene,2),lambda,0); %generating MRx3 gene indices | ||
save([matdir filesep 'MRx3_l90_human_geneinds.mat'],'geneinds'); | ||
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%DEFINING MAPPING PARAMETER INPUTS | ||
ng_param_list = [100:100:1000, size(regvgene,2)]; %values of nG to test and map, going through genes in MRx3 ranked order | ||
% ng_param_list = [50:10:1000, 1050:50:2000, 2100:100:3900, 4000:500:14500, size(regvgene,2)]; | ||
missmethod = 'MRx3'; %gene ranking/subsetting method as a label, options are 'MRx3' and 'none' | ||
infmethod = 'inv+res'; %inversion method between E and C*D, options are 'inversion', 'inv+res' to also get residuals, and 'corr' for correlation mapping | ||
savename = 'CellDensity_Human_allnG.mat'; %set name of file to be saved | ||
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%GENERATING MAPS, RESIDUALS, METADATA, & ELBOW INDEX/CURVE | ||
outstruct = Cell_Density_Outstruct_Human(genevct,regvgene,... | ||
gene_names,ng_param_list,lambda,missmethod,infmethod,... | ||
[],matdir); %getting outstruct of maps and residuals across nG | ||
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%DEFINING ELBOW | ||
makefig = 1; %binary flag whether or not to make elbow curve plot | ||
elbowind = elbow_selector_human(outstruct,makefig); %getting elbow index value and generating elbow curve | ||
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save([matdir filesep savename],'outstruct','ng_param_list','lambda',... %saving cell mapping output | ||
'missmethod','infmethod','geneinds','elbowind'); |