-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathsearchindex.js
More file actions
1 lines (1 loc) · 12.5 KB
/
searchindex.js
File metadata and controls
1 lines (1 loc) · 12.5 KB
1
Search.setIndex({objects:{"":{basicClusterHoehnerExampleData:[3,0,1,""],pyGCluster:[0,0,1,""],advancedClusterHoehnerExampleData:[3,0,1,""],simpleExpressionMap:[3,0,1,""],getpyGPickleInfo:[3,0,1,""],plotCommunities:[3,0,1,""],test_pyGCluster:[2,0,1,""]},pyGCluster:{Cluster:[0,3,1,""],create_default_alphabet:[0,2,1,""],yield_noisejected_dataset:[0,2,1,""],resampling_multiprocess:[0,2,1,""],seekAndDestry:[0,2,1,""]},"pyGCluster.Cluster":{load:[0,1,1,""],convergence_plot:[0,1,1,""],draw_expression_map_for_cluster:[0,1,1,""],create_rainbow_colors:[0,1,1,""],plot_nodetree:[0,1,1,""],plot_mean_distributions:[0,1,1,""],draw_community_expression_maps:[0,1,1,""],draw_expression_map_for_community_cluster:[0,1,1,""],delete_resampling_results:[0,1,1,""],plot_clusterfreqs:[0,1,1,""],resample:[0,1,1,""],save:[0,1,1,""],draw_expression_profiles:[0,1,1,""],build_nodemap:[0,1,1,""],do_it_all:[0,1,1,""],frequencies:[0,1,1,""],write_legend:[0,1,1,""],calculate_distance_matrix:[0,1,1,""],check_if_data_is_log2_transformed:[0,1,1,""],info:[0,1,1,""],draw_expression_map:[0,1,1,""],median:[0,1,1,""],write_dot:[0,1,1,""],check4convergence:[0,1,1,""]}},terms:{represent:[0,2],all:[0,4,2,3],code:[0,4],dist:2,edg:0,illustr:[0,2],skip:0,focus:0,yellow:[0,4],ibbp:2,secondli:2,signific:2,correl:[0,4,2],broader:[0,4],follow:[0,4,2],hoehner_dataset:3,row:0,hierarch:[0,2],content:[1,2],middl:2,depend:[4,2],omic:2,hierar:2,graph:2,decim:0,convergence_plot:[0,2,3],specif:[0,2],deviat:[0,4,2,3],min_obcofreq_2_plot:0,puor:0,under:2,sens:0,inject:[0,2],moclusterdirectori:0,sourc:[0,2],everi:4,string:[0,4],fals:0,functionalitycheck:[2,3],util:3,print:[0,4],pract:2,min_value_4_expression_map:[0,4],jgi4:0,condit:[0,4,2],veri:2,exact:2,induct:4,level:0,did:0,list:[0,4],prefix:0,iter:[0,2,3],correct:[2,3],draw_community_expression_map:[0,4],form:[0,2],examplefil:[2,3],sd23:[0,4],sd22:[0,4],sd21:4,prepar:4,pleas:[0,2,3],upper:0,smaller:[0,4,2],tel:2,seper:0,direct:[4,3],second:[0,4,2,3],doe:[0,4],pygclust:[0,1,2,3,4],download:[1,2],further:[0,4],spectral:0,index:[0,1],what:0,iter_top_p:0,compar:2,gansner:2,neg:0,section:[4,3],advanc:3,jaeger:2,children:0,cell:2,delet:0,heatmap:3,dendrogram:0,"new":[4,2],net:2,"public":[0,2],full:0,themselv:0,chose:0,whose:0,resampl:[0,4,2,3],"5gb":3,gener:[0,1,2,3,4],never:2,genet:2,here:[0,2],draw_expression_profil:[0,4],address:2,expression_map_filenam:0,ratio:[4,2,3],modifi:4,sinc:[0,2],valu:[0,4,3],box:[0,4,3],search:[0,1],larger:0,technolog:2,step:[0,4,2,3],muenster:2,queue:0,converg:[0,2,3],amount:0,implement:[0,1,2,4],gene:[0,2,3],commonli:2,via:[0,2],condition3:[0,4],appli:0,modul:[0,1],yield_noisejected_dataset:0,ask:[2,3],"boolean":0,visibl:2,instal:[1,2,3],softw:2,txt:0,increasing_min_overlap:0,highli:[0,2],plot:[0,1,2,3,4],fed:0,from:[0,1,2,3,4],describ:[0,3],would:[4,2,3],commun:[0,1,2,3,4],photosystem:4,univers:2,two:[0,2],workstat:4,process:[0,4,2,3],program:0,call:[0,4],taken:[4,2,3],mean12:[0,4],basi:3,type:0,until:[0,2,3],analyz:[4,2],sort:0,minim:4,fufezan:2,cytoscap:2,relat:[0,2],warn:4,visual:[0,1,2,3,4],examin:0,ward:[0,4],herebi:2,must:0,none:[0,4],graphic:0,retriev:[1,3],hour:3,setup:2,work:[0,4,2],annot:0,rdgy:0,remain:0,obvious:4,can:[0,4,2,3],simpleexpressionmap:3,root:[0,2],control:4,tar:2,give:0,threshold_4_the_lowest_max_freq:[0,4,3],hoehner_example_run:3,sudo:2,share:0,indic:[0,1,2,4],high:[0,2,3],critic:2,minimum:[0,4],want:[4,2,3],acclim:2,agement:2,pickle_filenam:[0,4],multipl:[0,2,3],paramert:0,divid:[0,2],rather:0,write:[0,4],how:[0,4,2,3],instead:0,csv:[0,3],simpl:[0,1,3,4],"\u03bc":2,updat:0,map:[0,1,2,3,4],plant:2,modern:0,max:4,after:[0,4,2,3],reflect:0,befor:[0,4],membership:[0,2],discard:[0,4],mai:[0,4],data:[0,1,2,3,4],demonstr:[1,2,3],man:2,ident:0,biotechnolog:2,essenti:4,draw_expression_map_for_clust:0,light:2,clusterfreqsmap_minsize4_top0clusters_top10promil:0,correspond:[0,4],assign:[0,4],issu:2,inform:[0,1,2,3],"switch":0,green:[0,4,2],frequent:[0,4,2,3],allow:0,enter:[2,3],min_cluster_s:[0,4],order:[0,4,2],unregul:4,approx:3,adjust:4,composit:[0,4,2],ahc:[0,2],over:4,top:[0,4,2,3],becaus:[0,4,2],testscript:[1,2,3],through:[0,2],"br\u00e9h\u00e9lin":2,nested_data_dict:[0,4],hierarchi:[0,4,2],still:0,vari:4,paramet:[0,4],style:[0,4,3],obcofreq:0,group:2,manuscript:3,fit:[0,4],chosen:2,window:[0,2],comprehens:2,therefor:4,might:2,them:2,evok:[0,4,2,3],"return":0,basicclusterhoehnerexampledata:3,thei:0,handl:2,plot_clusterfreq:[0,4],overal:4,initi:[0,4],number:[0,4,2,3],identifier1:[0,4],dataset:[0,2,3],bigger:0,introduct:[1,2],biomolecular:2,term:[0,2],document:[4,1,2],ordereddict:0,name:[0,4],edit:4,revers:2,loadedclust:0,myprofil:4,slide:0,test_pygclust:[2,3],arrow:2,each:[0,4,2,3],found:[0,2],complet:[0,4,2,3],side:0,mean:[0,4,2],christian:2,citat:[1,2],replac:[0,4],individu:0,genom:2,continu:[0,2,3],procedur:0,realli:0,cotain:[2,3],linkag:[0,4,2],meta:[0,2],expect:0,betweeen:0,extract:0,shannon:2,hoehner:[4,3],shown:[0,4,2],sd12:[0,4],network:2,sd11:[0,4],gradient:[0,4],open:2,publish:2,n_color:0,profil:[0,4,2,3],daniel:0,cpus_2_us:[0,4],rel:[0,4],pathtopygclusterpickl:3,uint32:0,red:[0,4],common:2,earlier:2,log2:[0,4],insid:0,workflow:[1,2],randonmli:[2,3],differ:[0,4,2,3],free:2,standard:[0,4,2,3],standalon:4,base:[0,2],dictionari:[0,4,3],latest:2,put:0,triangl:2,freq:0,combin:[0,2],afterward:0,rect:4,care:4,"_conpo":4,rdylgn:0,thread:[0,3],draw_expression_map:0,frequenc:[0,4,2,3],florida:2,minsize_resampl:4,filter:0,clusterclass:0,mean23:[0,4],mean22:[0,4],mean21:4,first:[0,4],origin:[0,4,2],softwar:2,rang:[0,4],directli:0,onc:[0,4],arrai:0,qualiti:4,hexcod:0,placehold:[0,4],exprof:0,done:[0,4],construct:[0,2],close2root:0,custom:2,miss:[0,4],predefin:4,sp3:2,size:[0,4],avail:[0,4,2,3],given:[0,4,3],"h\u00f6hner":2,script:[4,1,2,3],associ:0,licens:2,contact:2,system:[0,2],least:0,chical:2,draft:0,resampling_multiprocess:0,circl:2,termin:0,white:[0,4],"final":[0,4,2],store:[0,4],low:[0,2,3],additional_label:0,option:[0,4,2,3],merged_pygcluster_pkl_object:3,juli:2,copi:2,specifi:[0,4],pygcluster_resampl:[0,4],tree_filenam:0,kept:0,than:[0,4,2,3],std:4,target:0,photosynthesi:0,saeed:2,remov:0,example_1promille_commun:4,zero:0,"6gb":3,cite:2,incopor:3,info:[0,1,3],iron:2,were:[0,2,3],grei:0,colorbrewer2:4,seri:4,exhibit:0,"function":[0,1,2,3,4],comput:[0,2],close:[0,2],pass:0,ani:[0,4],packag:2,color_gradi:[0,4],have:[0,4,2,3],exper:2,need:0,consol:4,element:0,border:0,minu:0,box_styl:[0,4],strength:2,engin:2,squar:2,"_list":0,min:4,self:0,check_if_data_is_log2_transform:0,check4converg:0,note:[0,4,2,3],also:[0,4,3],without:0,take:[2,3],which:[0,4,2,3],environ:2,subject:[0,2],mit:2,singl:[0,3],dlc:[0,2],sure:[2,3],germani:2,distribut:[0,2],plenti:0,do_it_al:[0,4,3],pathtoexamplefil:3,object:[0,4,2,3],reach:[0,2,3],nodeid:0,multitud:0,most:[0,4,2,3],render:0,regular:[0,4],pair:0,"class":[0,4],appear:0,doc:0,request:0,drive:2,proteom:[4,2],pipe:0,agglom:[0,2],delete_resampling_result:0,determin:[0,3],pattern:[0,2],niehu:2,axi:0,dataq:0,dot:[0,4],gain:2,slope:0,upregul:4,show:[0,4,2,3],text:2,wehr:3,stringent:2,permiss:0,threshold:[0,4,2,3],uniform:0,pkl:[0,1,3,4],make:[2,3],current:[0,4],onli:[0,4],highest:0,locat:3,nois:[0,2],copyright:2,explain:4,solut:[0,4],figur:[4,2,3],should:[0,4,2,3],version:2,dict:[0,4],mean13:[0,4],chlamydomona:2,mean11:[0,4],basex:0,folder:[0,2,3],overwritten:4,reset:0,hit:[2,3],variou:3,get:[2,3],express:[0,1,2,3,4],stop:[0,2,3],joint:2,obviou:4,cannot:0,advancedclusterhoehnerexampledata:3,"import":[0,4,3],increas:[0,4,2],graphviz:[0,2],awai:4,requir:[0,4,2,3],estmat:0,reveal:2,iter_max:[0,4,2,3],synthet:[2,3],"1337_2":4,median:0,yield:[0,2],method:[0,4],whether:2,most_frequent_clust:0,integr:2,contain:[0,4,2,3],comma:0,where:[0,4,2],black:[0,4,2],fastclust:2,iter_window:0,set:[0,4,2],cond1:0,seq:2,cond2:0,"float":0,iterstep:[2,3],knowledg:0,maximum:[0,3],see:[0,4,2,3],result:[0,4,2,3],respons:2,defici:2,charact:0,best:0,concern:0,closer:2,statu:2,detect:[0,2],parent:0,correctli:0,matter:0,prgn:0,below:[0,4],label:0,nodemap:[0,1,3,4],enough:3,between:[0,2,3],drawn:0,pygcust:4,approach:2,email:2,attribut:0,altern:4,accord:0,august:2,kei:[0,4],numer:0,heightnew:4,extens:0,len:0,otherwis:[0,2,3],come:0,addit:0,both:[4,2],schlossplatz:2,data_tupl:0,last:2,equal:[0,4],force_plot:0,pdf:[0,2,3],uncertainti:2,com:2,condition2:[0,4],condition1:[0,4],load:[0,4],among:0,hold:0,simpli:[4,3],session:0,point:[0,2],color:[0,4,2],plot_mean_distribut:0,height:4,fastaid1:0,fastaid2:0,written:[0,4],draw:[0,4,2],suppli:4,averag:[0,4],typic:0,consider:4,save:[0,4,2,3],creat:[0,4,2],addition:[4,2,3],classic:[0,4],numpi:[0,2],three:0,been:0,mark:2,top_x_clust:[0,4,3],basic:[4,3],evalut:0,ram:3,regul:[4,2],presenc:[2,3],biotechniqu:2,convert:0,coordin:4,togeth:0,child:0,"_get_most_frequent_clust":0,oxfordjourn:2,former:0,those:0,statist:2,"case":[0,4],main:0,downregul:4,durat:3,lesser:0,defin:[0,4,2,3],calcul:0,pairwis:2,chlre4:0,create_default_alphabet:0,printabl:0,advantag:0,brewer:4,almost:0,metric:[0,4,2],tabl:1,henc:0,herein:0,cluster:[0,1,2,3,4],kwarg:4,protein:[0,4],mani:[4,2,3],cfreq:0,sever:4,greater:0,measur:2,microarrai:2,develop:[0,2],welcom:1,prior:4,perform:[0,2,3],alphabet:0,identifier2:[0,4],same:[0,2],python:[0,4,2],html:0,eventu:0,start:[0,4,2],higher:[4,2],iter_step:0,finish:[0,2,3],http:[0,4,2],structur:[0,4],closest:2,rainbow:0,nest:[0,4],wherea:3,pyglcust:2,temporari:0,user:[0,4],freeli:2,example_1promilleclusters_minsize4:4,iter_till_the_end:0,lower:0,appropri:0,off:0,transcriptom:4,firstli:2,entri:[0,4],thu:2,well:[0,4],inherit:0,pickl:[0,4],sd13:[0,4],exampl:[0,1,2,3,4],command:[4,2,3],thi:[0,4,2,3],choos:4,metabol:2,model:2,dimension:0,meet:2,distanc:[0,4,2],identifi:[0,4,2],rowpo:4,less:4,obtain:[0,4],shape:[0,2],assur:0,stringenc:[0,4],simultan:0,speed:[0,2],tca:0,rdylbu:0,widthnew:4,except:0,desktop:[0,4],rgb:[0,4],valid:[0,2],larg:[0,2],densiti:0,input:[0,4,2,3],subsequ:0,build:[0,4],applic:2,path_to_pygcluster_pkl_fil:4,format:[0,4],rna:2,varieti:0,multiprocess:0,fusion:0,mol:2,press:2,part:[0,4],glycolysi:0,getpygpickleinfo:3,python2:2,insert:0,stuff:4,like:[4,2,3],success:4,filenam:[0,4],manual:0,zoom:0,stroke:4,server:4,collect:0,examplescript:[2,3],necessari:[0,4],either:0,output:[0,4,3],page:1,supplementari:0,encount:0,www:2,working_directori:0,n_legend_nod:[0,4],deal:4,interv:0,interact:2,some:[0,4,2,3],back:0,intern:0,sampl:[0,2,3],respect:[0,2],insur:2,constitut:0,"m\u00fcllner":2,scale:0,bottom:2,normal:[0,4,2,3],definit:4,zerofactor:0,overlap:[0,2],estim:[0,4],centroid:0,select:0,plot_nodetre:0,brbg:0,dlc_freq_dict:0,reproduc:[0,2],refer:[0,1,2],defaultdict:0,max_value_4_expression_map:[0,4],run:[2,3],compris:0,tree:0,inspect:0,usag:[0,1,2,3,4],biologi:2,write_legend:0,post:2,euclidean:[0,4,2],chapter:4,sub:0,about:[0,4],tm4:2,zip:2,incorpor:4,materi:0,memori:[0,4],simul:0,degre:0,sub_fold:0,bz2:2,other:[0,2],routin:[0,2],own:[0,4,3],emphasi:0,within:4,encod:0,bound:0,latter:0,assess:[0,2],empti:0,ensur:2,chang:2,your:2,merg:[0,2],calculate_distance_matrix:0,institut:2,weight:0,wai:[0,4],pictur:0,bioinformat:2,execut:[4,2,3],support:0,clusterid:0,transform:0,fast:2,create_rainbow_color:0,communityclust:0,width:4,includ:[0,4],scalebyfreq:0,forward:0,machin:4,verbosity_level:0,analysi:[0,2],"\u03c3":2,properli:[2,3],north:2,build_nodemap:[0,4],offer:[0,2],tupl:[0,4],gaussian:0,github:2,cloud:0,link:4,piyg:0,branch:2,line:0,uni:2,"true":0,minfrequ_resampl:4,count:0,again:[0,4],algorithm:[0,1,2],consist:0,possibl:[0,4,3],"default":[0,4,2,3],minkowski:4,access:0,write_dot:[0,4],record:0,scipi:[0,4,2],mypath:4,highlight:0,more:0,connect:0,identifiern:0,featur:4,constant:0,evalu:0,clusterfreq:0,"int":0,certain:0,dure:0,novel:2,repres:[0,4,2],novemb:2,gephi:[0,4],file:[0,4,3],home:0,path:0,check:[0,1,2,3],fill:[0,4],barplot:0,min_overlap:0,titl:4,when:[0,4,2,3],rdbu:0,barth:2,declar:0,seekanddestri:0,rememb:0,spatial:[0,4],test:[2,3],you:[2,3],node:[0,4,2],variabl:0,stat:2,repeat:2,intend:0,reinhardtii:2,condens:0,function_2_generate_noise_injected_dataset:0,org:[0,4,2],initil:0,intens:0,consid:[0,2],rpy2:[0,2],expressionmap:4,plotcommun:3,iter_tol:0,matrix:0,reduc:[0,2],longer:[2,3],furthermor:0,min_cluster_freq_2_retain:0,directori:[0,4],svg:[0,4],draw_expression_map_for_community_clust:0,clusterfreqsmap:0,legend_filenam:0,time:[0,4],starting_min_overlap:0,agfufezan:2,legend:[0,4]},objtypes:{"0":"py:module","1":"py:method","2":"py:function","3":"py:class"},titles:["2. Module pyGCluster","Welcome to pyGCluster’s documentation!","1. Introduction","4. Example scripts","3. Usage"],objnames:{"0":["py","module","Python module"],"1":["py","method","Python method"],"2":["py","function","Python function"],"3":["py","class","Python class"]},filenames:["pyGCluster","index","intro","examples","usage"]})