submissionChanges

vicsanga · Mar 14, 2023 · b07fab1 · b07fab1
1 parent 1d98ff1
commit b07fab1
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Showing 12 changed files with 29 additions and 36 deletions.
diff --git a/Postre_app.zip b/Postre_app.zip
diff --git a/Postre_app/functions/RankingGenes_Deciphering_etiology.R b/Postre_app/functions/RankingGenes_Deciphering_etiology.R
@@ -530,6 +530,10 @@ rankingGenes<-function(genesData, phase, runMode, patientInfo){
           ##For those whose TAD is entirely duplicated we are not even considering where the enhancers are located
 
           if(info_gene[,"TypeDomainInitial"]=="TAD_disrupted"){
+            ###################################################
+            ## The gene is duplicated and its TAD is disrupted
+            ###################################################
+
             ##It will take into account nEnh before and after, as with LongRange translocation, inversion, or deletion
             gof_score_metadata_longRange<-eval_Gof_indirectEffect_score(matrixPhase = matrixPhase, 
                                                                         geneTransversalData = geneTransversalData,
@@ -542,9 +546,13 @@ rankingGenes<-function(genesData, phase, runMode, patientInfo){
             gof_score_longRange<-gof_score_metadata_longRange$finalScore
 
           }else{
+            ############################################
+            ##This means the WHOLE TAD IS DUPLICATED
+            ############################################
             ##We assign this score to 0, so that this can never be higher than the one by direct effect
             # gof_score_longRange<-0
             ##We assign this score to 0, so that this can never be higher than the one by direct effect
+
             gof_score_metadata_longRange<-list("finalScore"=0,
                                                "geneEnhancerScore"=NA,
                                                "genePhenoScore"=NA,
@@ -557,7 +565,7 @@ rankingGenes<-function(genesData, phase, runMode, patientInfo){
 
           }
 
-          ###SEGUIR POR AQUI, HE DE METER EL DE _METADATA Y LUEGO PILLAR EL VALOR DEL FINAL SCORE
+          ####Computing coding effect
           gof_score_metadata_directEffect<-eval_Gof_directEffect_score(matrixPhase = matrixPhase, 
                                                                        geneTransversalData = geneTransversalData,
                                                                        phenoScore = phenoScore_GOF,

diff --git a/Postre_app/functions/graphicalSummary_generation.R b/Postre_app/functions/graphicalSummary_generation.R
@@ -215,11 +215,9 @@ graphicalSummary_generation<-function(patientResults, minPathogenicScore){
               }else if((gene_mechanism=="LongRange_geneDuplication") || (gene_mechanism=="Direct_LongRange_geneDuplication")){
                 ##It is predicted in intra TAD SV a longRange_geneDuplication
                 ##Basically the gene is active and gets duplicated with some enhancers
-                ##But the gene is duplicated inside of the TAD, and based on the algorithm the gene has to be active
-                # Bec gene_breakpoint == "Break1&2"
-                ##So just paint the gene as duplicated
-
-                gene_breakp_line_type<-"surroundingGene"
+                #How to handle this scenario is done afterwards
+                #But it implies that the breakpoints have to be painted around the gene
+                geneBreakP_Position_respectToTSS<-"bothSides"##Particularities for this are considered afterwards in this script
 
               }else{
                 ##Just generating this variable to avoid missing variable errors
@@ -446,18 +444,14 @@ graphicalSummary_generation<-function(patientResults, minPathogenicScore){
 
                 if(((gene_mechanism == "LongRange_geneDuplication") || (gene_mechanism =="Direct_LongRange_geneDuplication")) && (SV_landing == "IntraTAD")){
 
-
-                  ##It means, okey, THE GENE IS DUPLICATED AND some enhancers  are duplicated surrounding the gene,
+                  ##It means, THE GENE IS DUPLICATED AND some enhancers  are duplicated surrounding the gene,
                   #And it has been predicted a pathomech where enh could contribute... bec they are dupl
-                  #but the gene is active since it is a pathogenically predicted intra TAD SV by GOF
-                  #So only plot the gene duplicated, keep it simple for now
-                  ##FUTURE, IMPROVE THIS PLOT
 
-                  ###For Now:
-                  ## Set n enhnacers initial and in the other TAD to 0
-                  ## If gene pathogenic effect by Direct Gene Truncation we do not care about enhancers
-                  ##So not painting them in the plot (achieved by enh = 0)
-                  ##But if in future we predict fusion transcripts... should be painted if that is the prediction
+                  ##################################################################
+                  ## IMPORTANT PARTICULARITIE. "nEnh_Kept...." tracks cognate enhancers, and nEnh_gained ectopic ones
+
+                  #Remembering the vars
+
                   # nEnh_initial_left
                   # nEnh_initial_right
                   # nEnh_other_domain
@@ -466,18 +460,15 @@ graphicalSummary_generation<-function(patientResults, minPathogenicScore){
                   # nEnh_kept_right
                   # nEnh_gained
 
-                  ##nEnhGained refers to ectopic enh, and this is an IntraTAD SV
-                  #So ignore
-                  ##################################################################
-                  ## IMPORTANT PARTICULARITIE. "Kept" tracks cognate enhancers 
-                  ## So if nkept > intial is because some of the initial duplicated
+                  ## So if nkept > initial is because some of the initial duplicated
 
+                  ##Tracking where to put the breakpoints regarding both sides of the gene
+                  ##Here we need to paint 2 breakpoints
                   gene_breakp_line_type<-list()
 
                   ##Tener en cuenta ambos breakpoints
                   ##For left breakp
                   if(nEnh_kept_left == nEnh_initial_left ){
-                    ##for now, does not matter wheter it had initially or not
                     gene_breakp_line_type$LeftBreakp<-"beforeTSS_duplic_none"##we will put the line between gene and enh
 
                   }else if(nEnh_kept_left == 2*nEnh_initial_left){
@@ -489,7 +480,6 @@ graphicalSummary_generation<-function(patientResults, minPathogenicScore){
 
                   ##For right Breakpoint
                   if(nEnh_kept_right == nEnh_initial_right){
-                    ##for now, does not matter wheter it had initially or not
                     gene_breakp_line_type$RightBreakp<-"afterTSS_duplic_none"##we will put the line between gene and enh
 
                   }else if(nEnh_kept_right == 2*nEnh_initial_right ){
@@ -623,11 +613,7 @@ graphicalSummary_generation<-function(patientResults, minPathogenicScore){
               fullOutpPath<-paste0(outpPath, gene,"_",targetMech, "_", phase,"_", patientResults$job_UniCode, ".png")
 
 
-
-
-
-              ##Do a try catch, If i get an error, just PLOT
-              ##Error on graphical abstract generation. Pq esto va a generar bastantes crasheos
+              ##Do a try catch, If i get an error, just PLOT "Error on graphical abstract generation".
 
               tryCatch({
 
@@ -825,8 +811,7 @@ graphicalSummary_generation<-function(patientResults, minPathogenicScore){
 
                   if(((gene_mechanism == "LongRange_geneDuplication") || (gene_mechanism =="Direct_LongRange_geneDuplication")) && (SV_landing == "IntraTAD")){
 
-                    # browser()
-
+                    #Two breakpoints around the gene are painted
                     info_drawingGENE_TAD<-paintGene_WT_TAD_intraTADdupWithEnh(tad_X_cord = tad_X_cord,
                                                                           tad_Y_cord = tad_YCoord_WildTypeLine,
                                                                           nEnh_initial_left = nEnh_initial_left, 
@@ -999,6 +984,7 @@ graphicalSummary_generation<-function(patientResults, minPathogenicScore){
 
                     }else{
                       ##Error, no concibo esta situacion ahora mismo
+                      ## Since regulatory domain stays the same
                       stop("I don't contemplate how this can happen sensibly right now")
                     }
 
@@ -1147,12 +1133,9 @@ graphicalSummary_generation<-function(patientResults, minPathogenicScore){
 
 
                   }else {
-                    #It would be intraTAD dup, where pathogenic mech by enh dup and not by gene dup
-                    #...rare, attending to what I have stated before
-                    ##Error, no concibo esta situacion ahora mismo
-                    # stop("I don't contemplate how this can happen sensibly right now")
-
-                    ##This is the SATB2 and FOXG1 situation where both scores are large buth long-range slightly larger...
+                    #It would be intraTAD dup, where  gene is duplicated and enh are also predicted to contribute
+                    ##This is the SATB2 and FOXG1 situation where both scores (coding and long-range) are large buth long-range slightly larger...
+                    #Painting just the duplicated gene to keep it simple
                     paint_Gene_Duplicated(gene = gene,
                                           xAxisLim = xAxisLim,
                                           tad_X_cord = tad_XCoord_OnCenter,

diff --git a/Postre_app/www/graphicalSummaries/FolderExp.txt b/Postre_app/www/graphicalSummaries/FolderExp.txt
@@ -0,0 +1,2 @@
+##Folder with automatically generated images for the analysed SV
+##Images will be removed upon job resubmission
diff --git a/...phicalSummaries/SATB2_20230314010450_Duplication_neurodevelopmental_TS_plot.png b/...phicalSummaries/SATB2_20230314010450_Duplication_neurodevelopmental_TS_plot.png
diff --git a/...mmaries/SATB2_20230314010450_Duplication_neurodevelopmental_polyCscore_plot.png b/...mmaries/SATB2_20230314010450_Duplication_neurodevelopmental_polyCscore_plot.png
diff --git a/...alSummaries/SATB2_GOF_PfcGw15_20230314010450_Duplication_neurodevelopmental.png b/...alSummaries/SATB2_GOF_PfcGw15_20230314010450_Duplication_neurodevelopmental.png
diff --git a/...F_PfcGw15_20230314010450_Duplication_neurodevelopmental_expressionLevelPlot.png b/...F_PfcGw15_20230314010450_Duplication_neurodevelopmental_expressionLevelPlot.png
diff --git a/...0314010450_Duplication_neurodevelopmental_regulatoryLandscapeBarplotChanges.png b/...0314010450_Duplication_neurodevelopmental_regulatoryLandscapeBarplotChanges.png
diff --git a/...alSummaries/SATB2_GOF_PfcGw18_20230314010450_Duplication_neurodevelopmental.png b/...alSummaries/SATB2_GOF_PfcGw18_20230314010450_Duplication_neurodevelopmental.png
diff --git a/...F_PfcGw18_20230314010450_Duplication_neurodevelopmental_expressionLevelPlot.png b/...F_PfcGw18_20230314010450_Duplication_neurodevelopmental_expressionLevelPlot.png
diff --git a/...0314010450_Duplication_neurodevelopmental_regulatoryLandscapeBarplotChanges.png b/...0314010450_Duplication_neurodevelopmental_regulatoryLandscapeBarplotChanges.png
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		##Folder with automatically generated images for the analysed SV
		##Images will be removed upon job resubmission