Develop DNA methylation plot and table API endpoints

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Develop DNA methylation plot and table API endpoints using the database schema and tables built in #69.

Following is a brief introduction on how to develop the DNA methylation plot and table API endpoints. The implementation of these procedures may require further discussions and modifications, to coordinate with #69 and the MTP web page design and development.

For each type of DNA methylation plot designed by @afarrel, a plot API endpoint and a table API endpoint need to be developed. The endpoints and R functions can take any appropriate names that are not taken by existing endpoints or functions. Following are the steps to add example gene_disease_dna_methylation plot and table endpoints:

• Install additionally required ubuntu and R packages in Dockerfile.

• Add src/get_dna_methylation_tbl.R to define a function, get_dna_methylation_tbl(ensg_id, efo_id), to retrieve a dataframe like object from the database.

  • src/get_gene_tpm_boxplot_tbl.R can be used as a reference for designing and implementing get_dna_methylation_tbl.
  • Query should be sent to the schema and table built in #69. If required data are absent, add a comment in #69 to describe what data are required.

• Add src/get_dna_methylation_plot.R to define a function, get_dna_methylation_plot(dna_methylation_table), to use the table returned by get_dna_methylation_tbl to generate a plot, which will be transferred to MTP.

• Add src/get_dna_methylation_summary_table.R to define a function, get_dna_methylation_summary_table(dna_methylation_table), to use the table returned by get_dna_methylation_tbl to generate a summary table, which will be transferred to MTP.

• Add the following code to main.R to source the defined functions in API HTTP server R runtime:

  source("src/get_dna_methylation_tbl.R")
  source("src/get_dna_methylation_plot.R")
  source("src/get_dna_methylation_summary_table.R")

• Add the following code in src/plumber.R to define a plot endpoint and a table endpoint.

  #* Get a single-gene single-disease DNA methylation table
  #*
  #* @tag "DNA methylation"
  #* @param ensemblId:str one gene ENSG ID.
  #* @param efoId:str one EFO ID.
  #* @serializer json
  #* @get /dna-methylation/gene-disease/json
  function(ensemblId, efoId) {
  dna_methylation_table <- get_dna_methylation_tbl(
    ensg_id = ensemblId, efo_id = efoId)
  
  dna_methylation_summary_table <- get_dna_methylation_summary_table(
    dna_methylation_table)
  
  return(dna_methylation_summary_table)
  }
  
  #* Get a single-gene single-disease DNA methylation plot
  #*
  #* @tag "DNA methylation"
  #* @param ensemblId:str one gene ENSG ID.
  #* @param efoId:str one EFO ID.
  #* @serializer png list(res = 300, width = 6000, height = 2700)
  #* @get /dna-methylation/gene-disease/plot
  function(ensemblId, efoId) {
  dna_methylation_table <- get_dna_methylation_tbl(
    ensg_id = ensemblId, efo_id = efoId)
  
  dna_methylation_plot <- get_dna_methylation_plot(
    dna_methylation_table)
  
  print(dna_methylation_plot)
  }

• Add the following code to tests/r_test_scripts/test_endpoint_http.R to add tests to the new endpoints:

  list(
  path = "/dna-methylation/gene-disease/plot",
  params = c("ensemblId", "efoId")),
  list(
  path = "/dna-methylation/gene-disease/json",
  params = c("ensemblId", "efoId")),

The newly added endpoints can be tested following the procedures described in README.md.

cc @afarrel @ewafula @chinwallaa