inst/scripts/query_all_datasets.R

In BD2K-DDI/ddiR: ddiR: The Omics Discovery Index R package

# This script search for all datasets and plot them by repository.
library(ddiR)
library(ggplot2)

query = "*:*";
datasets <- search.DatasetsSummary(query = query)
d <- data.frame(ID = character(),
               Database = character(),
               stringsAsFactors=FALSE)

colnames(d) <- c("ID", "Database")


index <- 1
datasetList <- vector("list", datasets@count)
for(datasetCount in seq(from = 0, to = datasets@count, by = 100)){
  datasets <- search.DatasetsSummary(query = query, start = datasetCount, size = 100)
  for(dataset in datasets@datasets){
    DatasetDetail = get.DatasetDetail(accession = dataset@dataset.id, database = dataset@database)
    if(!is.null(DatasetDetail)){
      d[nrow(d)+1, ] <- c(as.character(DatasetDetail@dataset.id), as.character(DatasetDetail@database))
      datasetList[[index]] <- DatasetDetail
      index <- index + 1
    }
  }
}

save(d, file="inst/data/datasets-d.RData")
save(datasetList, file="inst/data/datasets-list.RData")

DF <- as.data.frame(unclass(d))

plot <- ggplot(DF, aes(factor(DF$Database), fill = factor(DF$Database))) +
    geom_bar(alpha = .5) + scale_y_sqrt(breaks = c(100, 1000, 4000, 10000, 20000, 40000, 65000)) +
    labs(title = "Number of Omics Datasests by Respoitory", x = "Repositories/Databases", y = "Number of Datasets (sqrt scale)") +
	scale_fill_discrete(guide = guide_legend(NULL), labels = c("ArrayExpress", "ExpressionAtlas", "EGA", "GNPS", "GPMDB", "MassIVE", "Metabolights", "MetabolomeExpress", "MetabolomicsWorkbench", "PeptideAtlas", "PRIDE")) +
    theme(axis.ticks = element_blank(), axis.text.x = element_blank(), panel.background = element_blank())

png(file = "inst/imgs/datasets-by-repository.png", width = 800, height = 600)
plot(plot)
dev.off()