library(ddiR)
library(ggplot2)
load(file="inst/data/datasets-list.RData")
resultDatasetFrame <- data.frame(ID = character(),
Database = character(),
omicsType = character(),
Taxonomy = character(),
Organism = character(),
Disease = character(),
Tissue = character(),
Cell = character(),
Instrument = character(),
stringsAsFactors=FALSE)
colnames(resultDatasetFrame) <- c("ID", "Database",
"omicsType", "Taxonomy", "Organism",
"Disease", "Tissue", "Instrument")
for(datIndex in 1:length(datasetList)){
currentDataset <- datasetList[[datIndex]];
if(!is.null(currentDataset)){
if(currentDataset@dataset.id == "E-TABM-185"){
print(currentDataset)
}
omicsDF <- data.frame(ID = character(), Database = character(), Taxonomy = character(), Organism = character(), stringsAsFactors=FALSE);
colnames(omicsDF) <- c("ID", "Database","Taxonomy", "Organism")
if(is.null(currentDataset@organisms) || currentDataset@organisms == "Not available"){
omicsDF[nrow(omicsDF)+1, ] <- c(currentDataset@dataset.id, currentDataset@database, "NA", "NA");
}else{
for(index in 1: length(currentDataset@organisms)){
currentOrganism <- currentDataset@organisms[[index]];
omicsDF[nrow(omicsDF)+1, ] <- c(as.character(currentDataset@dataset.id), as.character(currentDataset@database), as.character(currentOrganism@accession), as.character(currentOrganism@name));
}
}
#print(omicsDF)
instrumentDF <- data.frame(ID = character(), Database = character(), Instrument = character(), stringsAsFactors=FALSE);
colnames(instrumentDF) <- c("ID", "Database","Instrument")
if(is.null(currentDataset@instruments) || currentDataset@instruments == "Not available"){
instrumentDF[nrow( instrumentDF)+1, ] <- c(currentDataset@dataset.id, currentDataset@database, "NA");
}else{
for(index in 1: length(currentDataset@instruments)){
currentInstrument <- currentDataset@instruments[[index]];
instrumentDF[nrow(instrumentDF)+1, ] <- c(as.character(currentDataset@dataset.id), as.character(currentDataset@database), as.character(currentInstrument));
}
}
#print(instrumentDF)
df <- merge(omicsDF, instrumentDF, by = c("ID", "Database"));
tissuesDF <- data.frame(ID = character(), Database = character(), Tissue = character(), stringsAsFactors=FALSE);
colnames(tissuesDF) <- c("ID", "Database","Tissue")
if(is.null(currentDataset@tissues) || currentDataset@tissues == "Not available"){
tissuesDF[nrow(tissuesDF)+1, ] <- c(currentDataset@dataset.id, currentDataset@database, "NA");
}else{
for(index in 1: length(currentDataset@tissues)){
currentTissue <- currentDataset@tissues[[index]];
tissuesDF[nrow(tissuesDF)+1, ] <- c(as.character(currentDataset@dataset.id), as.character(currentDataset@database), as.character(currentTissue));
}
}
df <- merge(df, tissuesDF, by = c("ID", "Database"));
diseaseDF <- data.frame(ID = character(), Database = character(), Disease = character(), stringsAsFactors=FALSE);
colnames(tissuesDF) <- c("ID", "Database","Disease")
if(is.null(currentDataset@diseases) || currentDataset@diseases == "Not available"){
diseaseDF[nrow(diseaseDF)+1, ] <- c(currentDataset@dataset.id, currentDataset@database, "NA");
}else{
for(index in 1: length(currentDataset@diseases)){
currentDisease <- currentDataset@tissues[[index]];
diseaseDF[nrow(diseaseDF)+1, ] <- c(as.character(currentDataset@dataset.id), as.character(currentDataset@database), as.character(currentDisease));
}
}
df <- merge(df, diseaseDF, by = c("ID", "Database"));
print(df)
}
}
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