R/drawORA.R
In CLippmann/ORA: Overrepresentation Analysis
Defines functions
drawORA
Documented in
drawORA
drawORA <- function(ORAresults, PlotFileWithExt, PlotDirectory, MarkDetails = TRUE, MarkHeadlines = TRUE, Overwrite=TRUE){
# To draw the gene ontology DAG containing ORA results' information.
# drawORA(ORAresults, PlotFileWithExt, PlotDirectory, MarkDetails = TRUE, MarkHeadlines = TRUE, Overwrite=TRUE)
# INPUT:
# ORAresults list of 4:
# LRNresults List of 16:
# Information needed to generate the lrn file containing all the calculated values for
# the GO terms found to be significant for input genes.
# LRNresults$GOtermNr Numeric; GO term numbers found to be significant for input genes.
# LRNresults$OntologyNr Numeric; Number of ontology (1=BP, 2=MF, 4=CC).
# LRNresults$NrOfGenesInUniverse Numeric; Number of genes in universe used for p-value computation.
# LRNresults$NrOfGenesInSample Numeric; Number of input genes used for p-value computation.
# LRNresults$NrOfAnnotationsInTerm Numeric; Number of annotations associated to GO term.
# LRNresults$Up Numeric; 1 if GO term is up regulated (expected < observed), 0 if down.
# LRNresults$ExpNrOfAnnsInTerm Numeric; Statistically expected number of genes annotated to GO term.
# LRNresults$ObservedNrOfAnnsInTerm Numeric; Empirically observed number of genes annotated to GO term.
# LRNresults$RelDiff Numeric; Relative difference of expected and observed in percent.
# LRNresults$Pvalue Numeric; Pvalues for each GO term received by statistical test.
# LRNresults$LogPvalue Numeric; log(Pvalues).
# LRNresults$Certainty Numeric; Certainty value. See function certainty.
# LRNresults$InfoValue Numeric; Value describing partial Shannon information. See infoValue.
# LRNresults$Remarkable Numeric; Product of Certainty and InfoValue.
# LRNresults$Importance Numeric; Minimum of Certainty and InfoValue.
# LRNresults$IsHeadline Boolean; 1 if GO term is headline, 0 if not.
# LRNresults$IsDetail Boolean; 1 if GO term is detail, 0 if not.
#
# NAMESresults List of 3:
# Information needed to generate the names file containing information about GO terms.
# NAMESresults$GOtermNr Numeric; GO term numbers found to be significant for input genes.
# NAMESresults$GOtermDescription String; Description of GO terms = termDescription(GOtermNr).
# NAMESresults$GOtermId String; GO term Id = termId(GOtermNr).
#
# Genes2GOtermsSparseMatrix Numeric; Sparse matrix explaining the connection of genes and GO terms.
# Genes2GOtermsSparseMatrix[i,3]==1 iff gene in ith row is annotated to
# GO term in ith row.
# GO2GOAdjMatrices List of 4:
# Adjacency matrices for each ontology and combined sparse matrix.
# GO2GOAdjMatrices$GO2GOAdjMatrix Numeric; Sparse adjacency matrix describing the complete directed
# acyclic graph (DAG) of the significant GOterms up to the root,
# i.e. the edges between GOterms and their parents. Dimnames of
# columes are specifying the Ontology - BP/MF/CC.
# GO2GOAdjMatrices$AdjMatrixGO2GOBP Numeric; (non-sparse) Adjacency matrix of BP-DAG.
# AdjMatrixGO2GOBP[i,j]==1 iff i is parent of j.
# GO2GOAdjMatrices$AdjMatrixGO2GOMF Numeric; (non-sparse) Adjacency matrix of MF-DAG.
# AdjMatrixGO2GOBP[i,j]==1 iff i is parent of j.
# GO2GOAdjMatrices$AdjMatrixGO2GOCC Numeric; (non-sparse) Adjacency matrix of CC-DAG.
# AdjMatrixGO2GOBP[i,j]==1 iff i is parent of j.
#
# PlotFileWithExt String;
# Name of the file that should be drawn with extension.
# Extension can be one of 'png', 'eps' or 'pdf'. Default is 'png'.
#
# OPTIONAL:
# PlotDirectory String; Default: current directory
# Directory where PlotFileWithExt should be saved.
# MarkDetails Boolean; Default: TRUE
# Set TRUE if details of DAG should be marked in blue colour.
# MarkHeadlines Boolean; Default: TRUE
# Set TRUE if headlines should be marked in yellow colour in DAG.
# Overwrite Boolean; Default: TRUE
# Set TRUE if existing files with the same name should be overwritten.
#
# OUTPUT:
# One up to three DAGs each saved in seperate file.
# AUTHOR:
# CL, 20.05.2016
# USES:
# functions:
# [1] "function" "do.call" "match" "if" "any"
# [6] "is.na" "warning" "termId" "length" "print"
# [11] "paste0" "basename" "file_path_sans_ext" "file_ext" "rep"
# [16] "as.logical" "termDescription" "plotGOgraph"
# Nach Ontologie aufschluesseln
AdjBP <- ORAresults$GO2GOAdjMatrices$AdjMatrixGO2GOBP
AdjMF <- ORAresults$GO2GOAdjMatrices$AdjMatrixGO2GOMF
AdjCC <- ORAresults$GO2GOAdjMatrices$AdjMatrixGO2GOCC
LrnResMatrix <- do.call(cbind, ORAresults$LRNresults)
# GOtermNr = GOtermNr,
# OntologyNr = ontologyNr(GOtermNr),
# NrOfGenesInUniverse = NrOfGenesInUniverse,
# NrOfGenesInSample = NrOfGenesInSample,
# NrOfAnnotationsInTerm = NrOfAnnotationsInTerm,
# Up = Up,
# ExpNrOfAnnsInTerm = ExpNrOfAnnsInTerm,
# ObservedNrOfAnnsInTerm = ObservedNrOfAnnsInTerm,
# RelDiff = RelDiff,
# Pvalue = Pvalues,
# LogPvalue = log(Pvalues),
# Certainty = Certainty,
# InfoValue = InfoValue,
# Remarkable = Remarkable,
# Importance = Importance,
# IsHeadline = IsHeadline,
# IsDetail = IsDetail
LrnResBP <- LrnResMatrix[ORAresults$LRNresults$OntologyNr==1,,drop=FALSE]
LrnResMF <- LrnResMatrix[ORAresults$LRNresults$OntologyNr==2,,drop=FALSE]
LrnResCC <- LrnResMatrix[ORAresults$LRNresults$OntologyNr==4,,drop=FALSE]
# Finde gemeinsame GOterme in Adj und LrnRes (in Adj sind ja auch noch die ergaenzten Eltern)
BPIndex <- match(LrnResBP[,'GOtermNr'], AdjBP$GOtermNrs) # Hier duerfen keine NAs drin sein
if(any(is.na(BPIndex))){warning('drawORA: NAs gefunden. Hier ist was kaputt. Das kann nicht sein!')}
MFIndex <- match(LrnResMF[,'GOtermNr'], AdjMF$GOtermNrs) # Hier duerfen keine NAs drin sein
if(any(is.na(MFIndex))){warning('drawORA: NAs gefunden. Hier ist was kaputt. Das kann nicht sein!')}
CCIndex <- match(LrnResCC[,'GOtermNr'], AdjCC$GOtermNrs) # Hier duerfen keine NAs drin sein
if(any(is.na(CCIndex))){warning('drawORA: NAs gefunden. Hier ist was kaputt. Das kann nicht sein!')}
# Parameter fuer plotGOgraph vorbereiten:
##### BP #####
Adj <- AdjBP$AdjMatrix
GOtermIDs <- termId(AdjBP$GOtermNrs)
if(length(GOtermIDs)==0){
print('drawORA: No GOterms in BP-DAG. Nothing to draw.')
}else{
PlotFile <- paste0(basename(tools::file_path_sans_ext(PlotFileWithExt)), '_BP.', file_ext(PlotFileWithExt))
# PlotDirectory <- PlotDirectory
Significant <- rep(0,length(GOtermIDs))
Significant[BPIndex] <- 1
IsHeadline <- rep(FALSE, length(GOtermIDs))
if(MarkHeadlines){
IsHeadline[BPIndex] <- as.logical(LrnResBP[,'IsHeadline'])
}# nur falls die markiert werden sollen den Wert angeben. Sonst alle auf Null lassen.
# MarkDetails <- MarkDetails
# Overwrite <- Overwrite
GOtermString <- termDescription(GOtermIDs)
Remarkable <- rep(0,length(GOtermIDs))
Remarkable[BPIndex] <- LrnResBP[,'Remarkable']
Pvalues <- rep(1,length(GOtermIDs))
Pvalues[BPIndex] <- LrnResBP[,'Pvalue']
NrGenesInTerm <- rep(NaN,length(GOtermIDs))
NrGenesInTerm[BPIndex] <- LrnResBP[,'NrOfAnnotationsInTerm']
Expected <- rep(0,length(GOtermIDs))
Expected[BPIndex] <- LrnResBP[,'ExpNrOfAnnsInTerm']
Observed <- rep(0,length(GOtermIDs))
Observed[BPIndex] <- LrnResBP[,'ObservedNrOfAnnsInTerm']
Importance <- rep(0,length(GOtermIDs))
Importance[BPIndex] <- LrnResBP[,'Importance']
Up <- rep(0,length(GOtermIDs))
Up[BPIndex] <- LrnResBP[,'Up']
plotGOgraph(Adj, GOtermIDs, PlotFile, PlotDirectory, Significant, IsHeadline, MarkDetails, Overwrite, GOtermString, Remarkable, Pvalues,NrGenesInTerm, Expected, Observed, Importance, Up)
}# end else von if(length(GOterms)==0)
# ##### MF #####
Adj <- AdjMF$AdjMatrix
GOtermIDs <- termId(AdjMF$GOtermNrs)
if(length(GOtermIDs)==0){
print('drawORA: No GOterms in MF-DAG. Nothing to draw.')
}else{
PlotFile <- paste0(basename(tools::file_path_sans_ext(PlotFileWithExt)), '_MF.', file_ext(PlotFileWithExt))
# PlotDirectory <- PlotDirectory
Significant <- rep(0,length(GOtermIDs))
Significant[MFIndex] <- 1
IsHeadline <- rep(FALSE, length(GOtermIDs))
if(MarkHeadlines){
IsHeadline[MFIndex] <- as.logical(LrnResMF[,'IsHeadline'])
}# nur falls die markiert werden sollen den Wert angeben. Sonst alle auf Null lassen.
# MarkDetails <- MarkDetails
# Overwrite <- Overwrite
GOtermString <- termDescription(GOtermIDs)
Remarkable <- rep(0,length(GOtermIDs))
Remarkable[MFIndex] <- LrnResMF[,'Remarkable']
Pvalues <- rep(1,length(GOtermIDs))
Pvalues[MFIndex] <- LrnResMF[,'Pvalue']
NrGenesInTerm <- rep(NaN,length(GOtermIDs))
NrGenesInTerm[MFIndex] <- LrnResMF[,'NrOfAnnotationsInTerm']
Expected <- rep(0,length(GOtermIDs))
Expected[MFIndex] <- LrnResMF[,'ExpNrOfAnnsInTerm']
Observed <- rep(0,length(GOtermIDs))
Observed[MFIndex] <- LrnResMF[,'ObservedNrOfAnnsInTerm']
Importance <- rep(0,length(GOtermIDs))
Importance[MFIndex] <- LrnResMF[,'Importance']
Up <- rep(0,length(GOtermIDs))
Up[MFIndex] <- LrnResMF[,'Up']
plotGOgraph(Adj, GOtermIDs, PlotFile, PlotDirectory, Significant, IsHeadline, MarkDetails, Overwrite, GOtermString, Remarkable, Pvalues,NrGenesInTerm, Expected, Observed, Importance, Up)
}# end else von if(length(GOtermIDs)==0)
# ##### CC #####
Adj <- AdjCC$AdjMatrix
GOtermIDs <- termId(AdjCC$GOtermNrs)
if(length(GOtermIDs)==0){
print('drawORA: No GOterms in CC-DAG. Nothing to draw.')
}else{
PlotFile <- paste0(basename(tools::file_path_sans_ext(PlotFileWithExt)), '_CC.', file_ext(PlotFileWithExt))
# PlotDirectory <- PlotDirectory
Significant <- rep(0,length(GOtermIDs))
Significant[CCIndex] <- 1
IsHeadline <- rep(FALSE, length(GOtermIDs))
if(MarkHeadlines){
IsHeadline[CCIndex] <- as.logical(LrnResCC[,'IsHeadline'])
}# nur falls die markiert werden sollen den Wert angeben. Sonst alle auf Null lassen.
# MarkDetails <- MarkDetails
# Overwrite <- Overwrite
GOtermString <- termDescription(GOtermIDs)
Remarkable <- rep(0,length(GOtermIDs))
Remarkable[CCIndex] <- LrnResCC[,'Remarkable']
Pvalues <- rep(1,length(GOtermIDs))
Pvalues[CCIndex] <- LrnResCC[,'Pvalue']
NrGenesInTerm <- rep(NaN,length(GOtermIDs))
NrGenesInTerm[CCIndex] <- LrnResCC[,'NrOfAnnotationsInTerm']
Expected <- rep(0,length(GOtermIDs))
Expected[CCIndex] <- LrnResCC[,'ExpNrOfAnnsInTerm']
Observed <- rep(0,length(GOtermIDs))
Observed[CCIndex] <- LrnResCC[,'ObservedNrOfAnnsInTerm']
Importance <- rep(0,length(GOtermIDs))
Importance[CCIndex] <- LrnResCC[,'Importance']
Up <- rep(0,length(GOtermIDs))
Up[CCIndex] <- LrnResCC[,'Up']
plotGOgraph(Adj, GOtermIDs, PlotFile, PlotDirectory, Significant, IsHeadline, MarkDetails, Overwrite, GOtermString, Remarkable, Pvalues,NrGenesInTerm, Expected, Observed, Importance, Up)
}# end else von if(length(GOtermIDs)==0)
}# end function drawORA
CLippmann/ORA documentation built on Feb. 4, 2020, 9:38 p.m.
R Package Documentation
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Defines functions drawORA
Documented in drawORA
drawORA <- function(ORAresults, PlotFileWithExt, PlotDirectory, MarkDetails = TRUE, MarkHeadlines = TRUE, Overwrite=TRUE){
# To draw the gene ontology DAG containing ORA results' information.
# drawORA(ORAresults, PlotFileWithExt, PlotDirectory, MarkDetails = TRUE, MarkHeadlines = TRUE, Overwrite=TRUE)
# INPUT:
# ORAresults list of 4:
# LRNresults List of 16:
# Information needed to generate the lrn file containing all the calculated values for
# the GO terms found to be significant for input genes.
# LRNresults$GOtermNr Numeric; GO term numbers found to be significant for input genes.
# LRNresults$OntologyNr Numeric; Number of ontology (1=BP, 2=MF, 4=CC).
# LRNresults$NrOfGenesInUniverse Numeric; Number of genes in universe used for p-value computation.
# LRNresults$NrOfGenesInSample Numeric; Number of input genes used for p-value computation.
# LRNresults$NrOfAnnotationsInTerm Numeric; Number of annotations associated to GO term.
# LRNresults$Up Numeric; 1 if GO term is up regulated (expected < observed), 0 if down.
# LRNresults$ExpNrOfAnnsInTerm Numeric; Statistically expected number of genes annotated to GO term.
# LRNresults$ObservedNrOfAnnsInTerm Numeric; Empirically observed number of genes annotated to GO term.
# LRNresults$RelDiff Numeric; Relative difference of expected and observed in percent.
# LRNresults$Pvalue Numeric; Pvalues for each GO term received by statistical test.
# LRNresults$LogPvalue Numeric; log(Pvalues).
# LRNresults$Certainty Numeric; Certainty value. See function certainty.
# LRNresults$InfoValue Numeric; Value describing partial Shannon information. See infoValue.
# LRNresults$Remarkable Numeric; Product of Certainty and InfoValue.
# LRNresults$Importance Numeric; Minimum of Certainty and InfoValue.
# LRNresults$IsHeadline Boolean; 1 if GO term is headline, 0 if not.
# LRNresults$IsDetail Boolean; 1 if GO term is detail, 0 if not.
#
# NAMESresults List of 3:
# Information needed to generate the names file containing information about GO terms.
# NAMESresults$GOtermNr Numeric; GO term numbers found to be significant for input genes.
# NAMESresults$GOtermDescription String; Description of GO terms = termDescription(GOtermNr).
# NAMESresults$GOtermId String; GO term Id = termId(GOtermNr).
#
# Genes2GOtermsSparseMatrix Numeric; Sparse matrix explaining the connection of genes and GO terms.
# Genes2GOtermsSparseMatrix[i,3]==1 iff gene in ith row is annotated to
# GO term in ith row.
# GO2GOAdjMatrices List of 4:
# Adjacency matrices for each ontology and combined sparse matrix.
# GO2GOAdjMatrices$GO2GOAdjMatrix Numeric; Sparse adjacency matrix describing the complete directed
# acyclic graph (DAG) of the significant GOterms up to the root,
# i.e. the edges between GOterms and their parents. Dimnames of
# columes are specifying the Ontology - BP/MF/CC.
# GO2GOAdjMatrices$AdjMatrixGO2GOBP Numeric; (non-sparse) Adjacency matrix of BP-DAG.
# AdjMatrixGO2GOBP[i,j]==1 iff i is parent of j.
# GO2GOAdjMatrices$AdjMatrixGO2GOMF Numeric; (non-sparse) Adjacency matrix of MF-DAG.
# AdjMatrixGO2GOBP[i,j]==1 iff i is parent of j.
# GO2GOAdjMatrices$AdjMatrixGO2GOCC Numeric; (non-sparse) Adjacency matrix of CC-DAG.
# AdjMatrixGO2GOBP[i,j]==1 iff i is parent of j.
#
# PlotFileWithExt String;
# Name of the file that should be drawn with extension.
# Extension can be one of 'png', 'eps' or 'pdf'. Default is 'png'.
#
# OPTIONAL:
# PlotDirectory String; Default: current directory
# Directory where PlotFileWithExt should be saved.
# MarkDetails Boolean; Default: TRUE
# Set TRUE if details of DAG should be marked in blue colour.
# MarkHeadlines Boolean; Default: TRUE
# Set TRUE if headlines should be marked in yellow colour in DAG.
# Overwrite Boolean; Default: TRUE
# Set TRUE if existing files with the same name should be overwritten.
#
# OUTPUT:
# One up to three DAGs each saved in seperate file.
# AUTHOR:
# CL, 20.05.2016
# USES:
# functions:
# [1] "function" "do.call" "match" "if" "any"
# [6] "is.na" "warning" "termId" "length" "print"
# [11] "paste0" "basename" "file_path_sans_ext" "file_ext" "rep"
# [16] "as.logical" "termDescription" "plotGOgraph"
# Nach Ontologie aufschluesseln
AdjBP <- ORAresults$GO2GOAdjMatrices$AdjMatrixGO2GOBP
AdjMF <- ORAresults$GO2GOAdjMatrices$AdjMatrixGO2GOMF
AdjCC <- ORAresults$GO2GOAdjMatrices$AdjMatrixGO2GOCC
LrnResMatrix <- do.call(cbind, ORAresults$LRNresults)
# GOtermNr = GOtermNr,
# OntologyNr = ontologyNr(GOtermNr),
# NrOfGenesInUniverse = NrOfGenesInUniverse,
# NrOfGenesInSample = NrOfGenesInSample,
# NrOfAnnotationsInTerm = NrOfAnnotationsInTerm,
# Up = Up,
# ExpNrOfAnnsInTerm = ExpNrOfAnnsInTerm,
# ObservedNrOfAnnsInTerm = ObservedNrOfAnnsInTerm,
# RelDiff = RelDiff,
# Pvalue = Pvalues,
# LogPvalue = log(Pvalues),
# Certainty = Certainty,
# InfoValue = InfoValue,
# Remarkable = Remarkable,
# Importance = Importance,
# IsHeadline = IsHeadline,
# IsDetail = IsDetail
LrnResBP <- LrnResMatrix[ORAresults$LRNresults$OntologyNr==1,,drop=FALSE]
LrnResMF <- LrnResMatrix[ORAresults$LRNresults$OntologyNr==2,,drop=FALSE]
LrnResCC <- LrnResMatrix[ORAresults$LRNresults$OntologyNr==4,,drop=FALSE]
# Finde gemeinsame GOterme in Adj und LrnRes (in Adj sind ja auch noch die ergaenzten Eltern)
BPIndex <- match(LrnResBP[,'GOtermNr'], AdjBP$GOtermNrs) # Hier duerfen keine NAs drin sein
if(any(is.na(BPIndex))){warning('drawORA: NAs gefunden. Hier ist was kaputt. Das kann nicht sein!')}
MFIndex <- match(LrnResMF[,'GOtermNr'], AdjMF$GOtermNrs) # Hier duerfen keine NAs drin sein
if(any(is.na(MFIndex))){warning('drawORA: NAs gefunden. Hier ist was kaputt. Das kann nicht sein!')}
CCIndex <- match(LrnResCC[,'GOtermNr'], AdjCC$GOtermNrs) # Hier duerfen keine NAs drin sein
if(any(is.na(CCIndex))){warning('drawORA: NAs gefunden. Hier ist was kaputt. Das kann nicht sein!')}
# Parameter fuer plotGOgraph vorbereiten:
##### BP #####
Adj <- AdjBP$AdjMatrix
GOtermIDs <- termId(AdjBP$GOtermNrs)
if(length(GOtermIDs)==0){
print('drawORA: No GOterms in BP-DAG. Nothing to draw.')
}else{
PlotFile <- paste0(basename(tools::file_path_sans_ext(PlotFileWithExt)), '_BP.', file_ext(PlotFileWithExt))
# PlotDirectory <- PlotDirectory
Significant <- rep(0,length(GOtermIDs))
Significant[BPIndex] <- 1
IsHeadline <- rep(FALSE, length(GOtermIDs))
if(MarkHeadlines){
IsHeadline[BPIndex] <- as.logical(LrnResBP[,'IsHeadline'])
}# nur falls die markiert werden sollen den Wert angeben. Sonst alle auf Null lassen.
# MarkDetails <- MarkDetails
# Overwrite <- Overwrite
GOtermString <- termDescription(GOtermIDs)
Remarkable <- rep(0,length(GOtermIDs))
Remarkable[BPIndex] <- LrnResBP[,'Remarkable']
Pvalues <- rep(1,length(GOtermIDs))
Pvalues[BPIndex] <- LrnResBP[,'Pvalue']
NrGenesInTerm <- rep(NaN,length(GOtermIDs))
NrGenesInTerm[BPIndex] <- LrnResBP[,'NrOfAnnotationsInTerm']
Expected <- rep(0,length(GOtermIDs))
Expected[BPIndex] <- LrnResBP[,'ExpNrOfAnnsInTerm']
Observed <- rep(0,length(GOtermIDs))
Observed[BPIndex] <- LrnResBP[,'ObservedNrOfAnnsInTerm']
Importance <- rep(0,length(GOtermIDs))
Importance[BPIndex] <- LrnResBP[,'Importance']
Up <- rep(0,length(GOtermIDs))
Up[BPIndex] <- LrnResBP[,'Up']
plotGOgraph(Adj, GOtermIDs, PlotFile, PlotDirectory, Significant, IsHeadline, MarkDetails, Overwrite, GOtermString, Remarkable, Pvalues,NrGenesInTerm, Expected, Observed, Importance, Up)
}# end else von if(length(GOterms)==0)
# ##### MF #####
Adj <- AdjMF$AdjMatrix
GOtermIDs <- termId(AdjMF$GOtermNrs)
if(length(GOtermIDs)==0){
print('drawORA: No GOterms in MF-DAG. Nothing to draw.')
}else{
PlotFile <- paste0(basename(tools::file_path_sans_ext(PlotFileWithExt)), '_MF.', file_ext(PlotFileWithExt))
# PlotDirectory <- PlotDirectory
Significant <- rep(0,length(GOtermIDs))
Significant[MFIndex] <- 1
IsHeadline <- rep(FALSE, length(GOtermIDs))
if(MarkHeadlines){
IsHeadline[MFIndex] <- as.logical(LrnResMF[,'IsHeadline'])
}# nur falls die markiert werden sollen den Wert angeben. Sonst alle auf Null lassen.
# MarkDetails <- MarkDetails
# Overwrite <- Overwrite
GOtermString <- termDescription(GOtermIDs)
Remarkable <- rep(0,length(GOtermIDs))
Remarkable[MFIndex] <- LrnResMF[,'Remarkable']
Pvalues <- rep(1,length(GOtermIDs))
Pvalues[MFIndex] <- LrnResMF[,'Pvalue']
NrGenesInTerm <- rep(NaN,length(GOtermIDs))
NrGenesInTerm[MFIndex] <- LrnResMF[,'NrOfAnnotationsInTerm']
Expected <- rep(0,length(GOtermIDs))
Expected[MFIndex] <- LrnResMF[,'ExpNrOfAnnsInTerm']
Observed <- rep(0,length(GOtermIDs))
Observed[MFIndex] <- LrnResMF[,'ObservedNrOfAnnsInTerm']
Importance <- rep(0,length(GOtermIDs))
Importance[MFIndex] <- LrnResMF[,'Importance']
Up <- rep(0,length(GOtermIDs))
Up[MFIndex] <- LrnResMF[,'Up']
plotGOgraph(Adj, GOtermIDs, PlotFile, PlotDirectory, Significant, IsHeadline, MarkDetails, Overwrite, GOtermString, Remarkable, Pvalues,NrGenesInTerm, Expected, Observed, Importance, Up)
}# end else von if(length(GOtermIDs)==0)
# ##### CC #####
Adj <- AdjCC$AdjMatrix
GOtermIDs <- termId(AdjCC$GOtermNrs)
if(length(GOtermIDs)==0){
print('drawORA: No GOterms in CC-DAG. Nothing to draw.')
}else{
PlotFile <- paste0(basename(tools::file_path_sans_ext(PlotFileWithExt)), '_CC.', file_ext(PlotFileWithExt))
# PlotDirectory <- PlotDirectory
Significant <- rep(0,length(GOtermIDs))
Significant[CCIndex] <- 1
IsHeadline <- rep(FALSE, length(GOtermIDs))
if(MarkHeadlines){
IsHeadline[CCIndex] <- as.logical(LrnResCC[,'IsHeadline'])
}# nur falls die markiert werden sollen den Wert angeben. Sonst alle auf Null lassen.
# MarkDetails <- MarkDetails
# Overwrite <- Overwrite
GOtermString <- termDescription(GOtermIDs)
Remarkable <- rep(0,length(GOtermIDs))
Remarkable[CCIndex] <- LrnResCC[,'Remarkable']
Pvalues <- rep(1,length(GOtermIDs))
Pvalues[CCIndex] <- LrnResCC[,'Pvalue']
NrGenesInTerm <- rep(NaN,length(GOtermIDs))
NrGenesInTerm[CCIndex] <- LrnResCC[,'NrOfAnnotationsInTerm']
Expected <- rep(0,length(GOtermIDs))
Expected[CCIndex] <- LrnResCC[,'ExpNrOfAnnsInTerm']
Observed <- rep(0,length(GOtermIDs))
Observed[CCIndex] <- LrnResCC[,'ObservedNrOfAnnsInTerm']
Importance <- rep(0,length(GOtermIDs))
Importance[CCIndex] <- LrnResCC[,'Importance']
Up <- rep(0,length(GOtermIDs))
Up[CCIndex] <- LrnResCC[,'Up']
plotGOgraph(Adj, GOtermIDs, PlotFile, PlotDirectory, Significant, IsHeadline, MarkDetails, Overwrite, GOtermString, Remarkable, Pvalues,NrGenesInTerm, Expected, Observed, Importance, Up)
}# end else von if(length(GOtermIDs)==0)
}# end function drawORA
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