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Author: PPKstar

DESCRIPTION

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+Package: scAnnotationBot
+Type: Package
+Title: Annotates cell clusters in single-cell sequencing analysis.
+Version: 1.0.0
+Author: Yikun Gao
+Maintainer: The package maintainer <www2405637072@163.com>
+Description: This package annotates cell clusters in single-cell sequencing analysis by using ERNIEBot or DashScope models.
+License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a license
+Encoding: UTF-8
+LazyData: true
+Imports: httr, jsonlite
+RoxygenNote: 7.2.3
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(DashScopeCellType)
+export(ERNIEBotCellType)
+
+importFrom(httr, POST, add_headers, content)
+importFrom(jsonlite, toJSON)
+importFrom(stats, setNames)

R/DashScope.R

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+#' @title Annotates cell clusters in single-cell sequencing analysis.
+
+#'
+
+#' @description This package annotates cell clusters in single-cell sequencing analysis by using ERNIEBot or DashScope models.
+
+#' @param api_key character. Obtained from the website https://dashscope.console.aliyun.com/apiKey.
+#' @param model character. Check from website https://dashscope.console.aliyun.com/billing, the default value is "qwen-max-longcontext".
+#' @param inputTable data.frame returned by FindAllMarkers.
+#' @param tissueName The tissue origin of single-cell sequencing data, such as "mouse brain".
+#' @param useGeneNumber numeric. The number of genes used for annotating cell types, with a default value of 10.
+
+#' @return character vector
+
+#' @export DashScopeCellType
+#' @name DashScopeCellType
+
+library(httr)
+library(jsonlite)
+DashScopeChat = function(api_key, contentText, model = "qwen-max-longcontext") {
+  url = 'https://dashscope.aliyuncs.com/api/v1/services/aigc/text-generation/generation'
+  headers = add_headers("Content-Type" = "application/json",
+                        "Authorization" = paste("Bearer", api_key))
+  json_input = list(
+    model = model,
+    input = list(
+      messages = list(
+        list(role = "system", content = "You are a tool used for annotating cell types in single-cell sequencing data, strictly executing annotation tasks according to the requirements!"),
+        list(role = "user", content = contentText)
+      )
+    ),
+    parameters = list(result_format = "message")
+  )
+  response = POST(url, headers, body = json_input, encode = "json")
+  response = content(response)
+  prompt_tokens = response$usage$input_tokens
+  completion_tokens = response$usage$output_tokens
+  total_tokens = response$usage$total_tokens
+  tokenMessage = paste0('Tokens usage report: ',
+                        '\n\t-prompt tokens: ',prompt_tokens,
+                        '\n\t-completion tokens: ',completion_tokens,
+                        '\n\t-total tokens: ',total_tokens,'\n')
+  cat(tokenMessage)
+  return(response$output$choices[[1]]$message$content)
+}
+
+DashScopeCellType = function(api_key = NULL, model = "qwen-max-longcontext", inputTable, tissueName = NULL, useGeneNumber = 5) {
+  if(is.null(api_key)) {
+    print('API key is not available!')
+    return()
+  }
+  clusterNum = length(levels(factor(inputTable$cluster)))
+  minCluster = as.numeric(levels(factor(inputTable$cluster))[1])
+  sectionSize = 30
+  sliceNum = ceiling(clusterNum/sectionSize)
+  responseList = list()
+  for (i in 1:sliceNum) {
+    cat(paste0('----------section ',i,' start----------\n'))
+    section = inputTable[inputTable$cluster<=sectionSize*i & inputTable$cluster>=minCluster+sectionSize*(i-1),]
+    markedClusters = tapply(section$gene, list(section$cluster), function(i) paste0(i[1:useGeneNumber], collapse = ","))
+    message = paste0("Use the following markers to identify the cell types of ", tissueName, " tissue cells. Provide only the cell type names in English, formatted as number followed by a colon and the cell type name in English, with no additional description after the name and the end of the response.",
+                     "\n", paste0(names(markedClusters), ":", unlist(markedClusters), collapse = "\n"))
+    response = DashScopeChat(api_key = api_key, content = message, model = model)
+    responseList = append(responseList, response)
+  }
+  combinedRes = paste(unlist(responseList), collapse = "\n")
+  clearedRes = gsub(pattern = "\n", replacement = "", x = combinedRes)
+  clearedRes = strsplit(clearedRes, "\\d+:")[[1]]
+  clearedRes = clearedRes[-1]
+  cellTypes = setNames(clearedRes, levels(factor(inputTable$cluster)))
+  return(cellTypes)
+}

R/ERNIEBot.R

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+#' @title Annotates cell clusters in single-cell sequencing analysis.
+
+#'
+
+#' @description This package annotates cell clusters in single-cell sequencing analysis by using ERNIEBot or DashScope models.
+
+#' @param account list. Obtained from the website https://console.bce.baidu.com/qianfan/ais/console/applicationConsole/application?_=1720524456151. client_id is the API Key, and client_secret is the Secret Key.
+#' @param model character. Check from website https://console.bce.baidu.com/qianfan/ais/console/onlineService. the default value is "completions_pro".
+#' @param inputTable data.frame returned by FindAllMarkers.
+#' @param tissueName The tissue origin of single-cell sequencing data, such as "mouse brain".
+#' @param useGeneNumber numeric. The number of genes used for annotating cell types, with a default value of 10.
+
+#' @return character vector
+
+#' @export ERNIEBotCellType
+#' @name ERNIEBotCellType
+
+library(httr)
+library(jsonlite)
+getAccessToken_ERNIEBot = function(client_id, client_secret) {
+  url = 'https://aip.baidubce.com/oauth/2.0/token'
+  headers = c('Content-Type' = 'application/json')
+  body = list(grant_type = 'client_credentials',
+              client_id = client_id,
+              client_secret = client_secret)
+  response = POST(url, add_headers(headers), body = body)
+  access_token = content(response)$access_token
+  return(access_token)
+}
+
+ERNIEBotChat = function(access_token, contentText, model = "completions_pro") {
+  url = paste0('https://aip.baidubce.com/rpc/2.0/ai_custom/v1/wenxinworkshop/chat/',model)
+  full_url = paste0(url, "?access_token=", access_token)
+  headers = c('Content-Type' = 'application/json')
+  data = list(
+    messages = list(
+      list(role = "user", content = contentText)
+    ),
+    system = 'You are a tool used for annotating cell types in single-cell sequencing data, strictly executing annotation tasks according to the requirements!'
+  )
+  json_data = toJSON(data, auto_unbox = TRUE)
+  response = POST(full_url, add_headers(headers), body = json_data)
+  response = content(response)
+  prompt_tokens = response$usage$prompt_tokens
+  completion_tokens = response$usage$completion_tokens
+  total_tokens = response$usage$total_tokens
+  tokenMessage = paste0('Tokens usage report: ',
+                        '\n\t-prompt tokens: ',prompt_tokens,
+                        '\n\t-completion tokens: ',completion_tokens,
+                        '\n\t-total tokens: ',total_tokens, '\n')
+  cat(tokenMessage)
+  return(response$result)
+}
+
+ERNIEBotCellType = function(account = list(client_id = NULL, client_secret = NULL), model = "completions_pro", inputTable, tissueName = NULL, useGeneNumber = 5) {
+  if(is.null(account$client_id) || is.null(account$client_secret)) {
+    print('client_id or client_secret is not available!')
+    return()
+  }
+  access_token = getAccessToken_ERNIEBot(client_id = account$client_id, client_secret = account$client_secret)
+  clusterNum = length(levels(factor(inputTable$cluster)))
+  minCluster = as.numeric(levels(factor(inputTable$cluster))[1])
+  sectionSize = 30
+  sliceNum = ceiling(clusterNum/sectionSize)
+  responseList = list()
+  for (i in 1:sliceNum) {
+    cat(paste0('----------section ',i,' start----------\n'))
+    section = inputTable[inputTable$cluster<=sectionSize*i & inputTable$cluster>=minCluster+sectionSize*(i-1),]
+    markedClusters = tapply(section$gene, list(section$cluster), function(i) paste0(i[1:useGeneNumber], collapse = ","))
+    message = paste0("Use the following markers to identify the cell types of ", tissueName, " tissue cells. Provide only the cell type names in English, formatted as number followed by a colon and the cell type name in English, with no additional description after the name and the end of the response.",
+                     "\n", paste0(names(markedClusters), ":", unlist(markedClusters), collapse = "\n"))
+    response = ERNIEBotChat(access_token = access_token, content = message, model = model)
+    responseList = append(responseList, response)
+  }
+  combinedRes = paste(unlist(responseList), collapse = "\n")
+  clearedRes = gsub(pattern = "\n", replacement = "", x = combinedRes)
+  clearedRes = strsplit(clearedRes, "\\d+:")[[1]]
+  clearedRes = clearedRes[-1]
+  cellTypes = setNames(clearedRes, levels(factor(inputTable$cluster)))
+  return(cellTypes)
+}

man/DashScopeCellType.Rd

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

man/ERNIEBotCellType.Rd

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+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/tests.html
+# * https://testthat.r-lib.org/reference/test_package.html#special-files
+
+library(testthat)
+library(scAnnotationBot)
+
+test_check("scAnnotationBot")

scAnnotationBot.Rproj

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+test_that("multiplication works", {
+  expect_equal(2 * 2, 4)
+})