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api.R

Copyright 2013 Allen Institute for Brain Science Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

 

      		
    

    

      
        

          
        

        
A function returning the path of the API.

      		
      
        
getApiPath <- function() {
  return("http://api.brain-map.org")
}

      		
    

    

      
        

          
        

        
Download all of the rows available from a supplied API query.  

      		
      
        
apiQuery <- function(query) {
  totalRows <- -1
  rowsPerPage <- 2000
  startRow <- 0
  queryFormat <- "%s/api/v2/data/%s&startRow=%d&numRows=%d"

      		
    

    

      
        

          
        

        
Download meta information about the human microarray samples one page at a time. 

      		
      
        
  while (totalRows < 0 || startRow < totalRows) {
    queryString <- sprintf(queryFormat, getApiPath(), query, startRow, rowsPerPage)
    print(queryString)
    
    resultString <- readLines(queryString)
    resultJSON <- fromJSON(resultString)
  
    if (totalRows < 0) {
      totalRows <- as.integer(resultJSON$total_rows)
      output <- resultJSON$msg
    } else {
      output <- c(output,resultJSON$msg)
    }

    startRow <- startRow + rowsPerPage
  }

  return(output)
}

      		
    

    

      
        

          
        

        
Download metadata about a specified structure.

      		
      
        
downloadStructure <- function(structureID) {
  queryString <- sprintf("%s/api/v2/data/Structure/%s.json", getApiPath(), structureID)
  print(queryString)
  resultString <- readLines(queryString)
  resultJSON <- fromJSON(resultString)
  
  return(resultJSON$msg[[1]])
}

      		
    

    

      
        

          
        

        
Sort a data frame full of sample meta information.

      		
      
        
downloadSampleProperties <- function(sampleInfo) {
  structureIDs = sampleInfo$structure_id
  numSamples <- length(structureIDs)

      		
    

    

      
        

          
        

        
Fill the sample data frame with color and order information.


      		
      
        
  structureColors <- array("#000000FF",numSamples)
  structureOrders <- array(0,numSamples)

  for (i in 1:numSamples) {
    s = downloadStructure(structureIDs[i])
    structureOrders[i] <- s$graph_order
    structureColors[i] <- paste("#",s$color_hex_triplet,sep="")
  }

  sampleInfo[,"order"] <- structureOrders
  sampleInfo[,"color"] <- structureColors
  return(sampleInfo)
}