Merge pull request #25 from CRI-iAtlas/develop

Develop

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: iatlasGraphQLClient
 Title: iatlas API Client
 Type: Package
-Version: 0.2.2
+Version: 0.2.4
 Author: Andrew Lamb
 Maintainer: Andrew Lamb <[email protected]>
 Description: This package is am R Client library for the iAtlas API.

R/api_cell_stats_queries.R

@@ -0,0 +1,38 @@
+#' Query Cell Stats
+#'
+#' @param entrez A vector integers
+#' @param paging A named list
+#' @param ... Arguments to create_result_from_api_query
+#' @export
+query_cell_stats <- function(
+  entrez = NA,
+  paging = NA,
+  ...
+){
+  tbl <- create_result_from_cursor_paginated_api_query(
+    query_args =  list(
+      "entrez" = entrez,
+      "paging" = paging,
+      "distinct" = F
+    ),
+    query_file = "cell_stats.txt",
+    default_tbl = dplyr::tibble(
+      "type" = character(),
+      "count" = integer(),
+      "avg_expr" = double(),
+      "perc_expr" = double(),
+      "dataset_name"  = character(),
+      "gene_entrez" = integer()
+    ),
+    select_cols = c(
+      "type",
+      "count",
+      "avg_expr" = "avgExpr",
+      "perc_expr" = "percExpr",
+      "dataset_name"  = "dataSet.name",
+      "gene_entrez" = "gene.entrez"
+    ),
+    ...
+  )
+  return(tbl)
+}

R/api_cells_queries.R

@@ -0,0 +1,140 @@
+#' Query Cells
+#'
+#' @param cohort A vector of characters
+#' @param cell A vector of characters
+#' @param paging A named list
+#' @param ... Arguments to create_result_from_api_query
+#' @export
+query_cells <- function(
+  cohort = NA,
+  cell = NA,
+  paging = NA,
+  ...
+){
+  tbl <- create_result_from_cursor_paginated_api_query(
+    query_args =  list(
+      "cohort" = cohort,
+      "cell" = cell,
+      "paging" = paging,
+      "distinct" = F
+    ),
+    query_file = "cells.txt",
+    default_tbl = dplyr::tibble(
+      "type" = character(),
+      "name" = character(),
+    ),
+    select_cols = c(
+      "type",
+      "name"
+    ),
+    ...
+  )
+  return(tbl)
+}
+
+#' Query SingleCellSeq
+#'
+#' @param entrez A vector integers
+#' @param cohort A vector of characters
+#' @param cell A vector of characters
+#' @param paging A named list
+#' @param ... Arguments to create_result_from_api_query
+#' @export
+query_single_cell_seq <- function(
+    entrez = NA,
+    cohort = NA,
+    cell = NA,
+    paging = NA,
+    ...
+){
+  tbl <- create_result_from_cursor_paginated_api_query(
+    query_args =  list(
+      "entrez" = entrez,
+      "cohort" = cohort,
+      "cell" = cell,
+      "paging" = paging,
+      "distinct" = F
+    ),
+    query_file = "single_cell_seq.txt",
+    default_tbl = dplyr::tibble(
+      "cell_type" = character(),
+      "cell_name" = character(),
+      "gene_entrez" = integer(),
+      "gene_hgnc" = character(),
+      "gene_single_cell_seq" = double()
+    ),
+    select_cols = c(
+      "cell_type" = "type",
+      "cell_name" = "name",
+      "genes"
+    ),
+    ...
+  )
+  if (nrow(tbl) == 0) return(tbl)
+  else {
+    tbl <- tbl %>%
+      tidyr::unnest(cols = "genes", keep_empty = T) %>%
+      dplyr::select(
+        "cell_type",
+        "cell_name",
+        "gene_entrez" = "entrez",
+        "gene_hgnc" = "hgnc",
+        "gene_single_cell_seq" = "singleCellSeq"
+      )
+  }
+  return(tbl)
+}
+
+
+#' Query SingleCellFeature
+#'
+#' @param feature A vector of characters
+#' @param cohort A vector of characters
+#' @param cell A vector of characters
+#' @param paging A named list
+#' @param ... Arguments to create_result_from_api_query
+#' @export
+query_single_cell_feature <- function(
+    feature = NA,
+    cohort = NA,
+    cell = NA,
+    paging = NA,
+    ...
+){
+  tbl <- create_result_from_cursor_paginated_api_query(
+    query_args =  list(
+      "feature" = feature,
+      "cohort" = cohort,
+      "cell" = cell,
+      "paging" = paging,
+      "distinct" = F
+    ),
+    query_file = "single_cell_feature.txt",
+    default_tbl = dplyr::tibble(
+      "cell_type" = character(),
+      "cell_name" = character(),
+      "feature_name" = character(),
+      "feature_display" = character(),
+      "feature_value" = double()
+    ),
+    select_cols = c(
+      "cell_type" = "type",
+      "cell_name" = "name",
+      "features"
+    ),
+    ...
+  )
+  if (nrow(tbl) == 0) return(tbl)
+  else {
+    tbl <- tbl %>%
+      tidyr::unnest(cols = "features", keep_empty = T) %>%
+      dplyr::select(
+        "cell_type",
+        "cell_name",
+        "feature_name" = "name",
+        "feature_display" = "display",
+        "feature_value" = "value",
+      )
+  }
+  return(tbl)
+}

R/api_features_queries.R

@@ -118,6 +118,64 @@ query_feature_values <- function(
   }
 }
 
+
+#' Query PseudoBulk Feature Values
+#'
+#' @param cohorts A vector of strings
+#' @param features A vector of strings
+#' @param paging A named list
+#' @param ... Arguments to create_result_from_api_query
+#' @export
+#' @importFrom magrittr %>%
+query_pseudobulk_feature_values <- function(
+    cohorts = NA,
+    features = NA,
+    paging = NA,
+    ...
+){
+  tbl <- create_result_from_cursor_paginated_api_query(
+    query_args =  list(
+      "cohort" = cohorts,
+      "feature" = features,
+      "paging" = paging,
+      "distinct" = F
+    ),
+    query_file = "pseudobulk_feature_values.txt",
+    default_tbl = dplyr::tibble(
+      "feature_name" = character(),
+      "feature_display" = character(),
+      "feature_order" = integer(),
+      "feature_class" = character(),
+      "cell_name" = character(),
+      "cell_type"= character(),
+      "value" = double()
+    ),
+    select_cols = c(
+      "feature_name" = "name",
+      "feature_display" = "display",
+      "feature_order" = "order",
+      "feature_class" = "class",
+      "cellTypeSamples"
+    ),
+    ...
+  )
+  if (nrow(tbl) == 0) return(tbl)
+  else {
+    tbl %>%
+      tidyr::unnest(cols = "cellTypeSamples", keep_empty = T) %>%
+      dplyr::select(
+        "feature_name",
+        "feature_display",
+        "feature_order",
+        "feature_class",
+        "cell_name" = "name",
+        "cell_type" = "cellType",
+        "value"
+      )
+  }
+}
+
+
 #' Query Features Range
 #'
 #' @param cohorts A vector of strings

R/api_genes_queries.R

@@ -276,3 +276,56 @@ query_gene_nanostring_expression <- function(
             )
     }
 }
+
+#' Query Pseudobulk Expression
+#'
+#' @param cohorts A vector of strings
+#' @param entrez A vector of integers
+#' @param paging A named list
+#' @param ... Arguments to create_result_from_api_query
+#'
+#' @export
+#' @importFrom magrittr %>%
+#' @importFrom rlang .data
+query_pseudobulk_expression <- function(
+    cohorts = NA,
+    entrez = NA,
+    paging = NA,
+    ...
+){
+  tbl <- create_result_from_cursor_paginated_api_query(
+    query_args = list(
+      "cohort" = cohorts,
+      "entrez" = entrez,
+      "paging" = paging,
+      "distinct" = F
+    ),
+    query_file = "pseudobulk_expression.txt",
+    default_tbl = dplyr::tibble(
+      "gene_entrez" = integer(),
+      "gene_hgnc" = character(),
+      "cell_name" = character(),
+      "cell_type" = character(),
+      "single_cell_seq_sum" = double()
+    ),
+    select_cols = c(
+      "gene_entrez" = "entrez",
+      "gene_hgnc" = "hgnc",
+      "cellTypeSamples"
+    ),
+    ...
+  )
+  if (nrow(tbl) == 0) return(tbl)
+  else {
+    tbl %>%
+      tidyr::unnest(cols = "cellTypeSamples", keep_empty = T) %>%
+      dplyr::select(
+        "gene_entrez",
+        "gene_hgnc",
+        "cell_name" = "name",
+        "cell_type" = "cellType",
+        "single_cell_seq_sum" = "singleCellSeqSum"
+      )
+  }
+}
+

inst/queries/cell_stats.txt

@@ -0,0 +1,32 @@
+query CellStats(
+    $paging: PagingInput
+    $distinct:Boolean
+    $entrez: [Int!]
+) {
+    cellStats(
+        paging: $paging
+        distinct: $distinct
+        entrez: $entrez
+    ) {
+        items {
+            dataSet { name }
+            gene { entrez }
+            type
+            count
+            avgExpr
+            percExpr
+        }
+        paging {
+            type
+            pages
+            total
+            startCursor
+            endCursor
+            hasPreviousPage
+            hasNextPage
+            page
+            limit
+        }
+        error
+    }
+}

inst/queries/cells.txt

@@ -0,0 +1,30 @@
+query Cells(
+      $paging: PagingInput
+      $distinct:Boolean
+      $cohort: [String!]
+      $cell: [String!]
+  ) {
+      cells(
+          paging: $paging
+          distinct: $distinct
+          cohort: $cohort
+          cell: $cell
+      ) {
+        items {
+            name
+            type
+        }
+        paging {
+            type
+            pages
+            total
+            startCursor
+            endCursor
+            hasPreviousPage
+            hasNextPage
+            page
+            limit
+        }
+        error
+    }
+}