fix some bugs

.Rhistory

@@ -0,0 +1,12 @@
+devtools::document()
+devtools::document()
+devtools::document()
+devtools::build()
+devtools::check()
+setwd("E:/CellTypeGPT-master")
+devtools::document()
+devtools::document()
+build()
+devtools::build()
+devtools::check()
+remotes::install_github("XWcode11/CellTypeGPT")

DESCRIPTION

@@ -1,14 +1,11 @@
 Package: CellTypeGPT
-Title: What the Package Does (One Line, Title Case)
-Version: 0.0.0.9000
-Authors@R: 
-    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "YOUR-ORCID-ID"))
-Description: What the package does (one paragraph).
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
+Type: Package
+Title: Annotate Cell Types using Custom GPT
+Version: 0.1.0
+Author: Your Name
+Maintainer: Your Name <[email protected]>
+Description: This package provides functions to annotate cell types using custom GPT models.
+License: MIT
+Imports: httr2
 Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Imports:
-    httr2

NAMESPACE

@@ -1,3 +1,3 @@
 # Generated by roxygen2: do not edit by hand
 
-export(CellTypeGPT)
+export(annotate_cell_types)

R/CellTypeGPT.R

@@ -1,5 +1,3 @@
-
-
 #' Annotate Cell Types using Custom GPT
 #'
 #' This function annotates cell types based on input gene markers.
@@ -8,41 +6,44 @@
 #' @param tissuename A character string specifying the tissue name.
 #' @param model A character string specifying the model to use.
 #' @param topgenenumber An integer specifying the number of top genes to consider.
-#' @param baseurl A character string specifying the base URL for the API. Default is "https://api.default.com/v1/chat/completions".
+#' @param api_base A character string specifying the base URL for the API.
 #' @return A character vector of annotated cell types.
 #' @export
-#' @name CellTypeGPT
+#' @name annotate_cell_types
+#' @examples
+#' # Example usage:
+#' # annotate_cell_types(input = my_gene_data, tissuename = "liver", model = "gpt-4o", topgenenumber = 10, api_base = "https://api.default.com/v1/chat/completions")
 
 library(httr2)
 
 
 annotate_cell_types <- function(input, tissuename = NULL, model = 'gpt-4o', topgenenumber = 10, api_base) {
   OPENAI_API_KEY <- Sys.getenv("OPENAI_API_KEY")
-  
+
   if (OPENAI_API_KEY == "") {
     stop("OpenAI API key not found. Please set your API key in the environment.")
   }
-  
+
 
   if (class(input) == 'list') {
     input <- sapply(input, paste, collapse = ',')
   } else {
     input <- input[input$avg_log2FC > 0, , drop = FALSE]
     input <- tapply(input$gene, list(input$cluster), function(i) paste0(i[1:topgenenumber], collapse = ','))
   }
-  
+
   cutnum <- ceiling(length(input) / 30)
   if (cutnum > 1) {
-    cid <- as.numeric(cut(1:length(input), cutnum))	
+    cid <- as.numeric(cut(1:length(input), cutnum))
   } else {
     cid <- rep(1, length(input))
   }
-  
+
   allres <- sapply(1:cutnum, function(i) {
     id <- which(cid == i)
     flag <- 0
     while (flag == 0) {
-       
+
       req <- request(api_base) %>%
         req_method("POST") %>%
         req_headers(
@@ -56,10 +57,10 @@ annotate_cell_types <- function(input, tissuename = NULL, model = 'gpt-4o', topg
             content = paste0('You are an expert in cell biology. Identify cell types of ', tissuename, ' cells using the following markers separately for each\n row. Only provide the cell type name. Do not show numbers or additional text before the name.\n Some can be a mixture of multiple cell types.\n', paste(input[id], collapse = '\n'))
           ))
         ))
-      
-      
+
+
       resp <- req_perform(req)
-      
+
       content <- resp_body_json(resp)
       res <- strsplit(content$choices[[1]]$message$content, '\n')[[1]]
 
@@ -70,8 +71,7 @@ annotate_cell_types <- function(input, tissuename = NULL, model = 'gpt-4o', topg
     names(res) <- names(input)[id]
     res
   }, simplify = FALSE)
-
-  print('Note: It is always recommended to check the results returned by GPT in case of\n AI hallucination, before going to downstream analysis.')
+  print('DONE.')
   return(gsub(',$', '', unlist(allres)))
 }