Fix issue with marker genes (#26)

* Update cytetype.R

* Update .gitignore

* Update client.R

* clickable report link

* error catch marker genes

* Increment version number to 0.1.4

Author: suu-yi

.gitignore

@@ -8,3 +8,4 @@
 .quarto
 revdep/
 inst/doc
+CyteTypeR.Rproj

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CyteTypeR
 Title: CyteType for R
-Version: 0.1.3
+Version: 0.1.4
 Description: CyteTypeR is the R version of CyteType python package.'
 Authors@R: 
     person("Nygen Analytics AB", , ,"contact@nygen.io", role = c("aut", "cre"))

NAMESPACE

@@ -10,6 +10,8 @@ importFrom(Seurat,AddMetaData)
 importFrom(Seurat,Embeddings)
 importFrom(Seurat,GetAssayData)
 importFrom(dplyr,"%>%")
+importFrom(dplyr,arrange)
+importFrom(dplyr,desc)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,slice_head)

R/client.R

@@ -2,7 +2,7 @@
 .submit_job <- function(payload, api_url, auth_token = NULL){
 
   submit_url <- file.path(api_url, "annotate")
-  log_info("Submitting job to API {api_url}")
+  log_info("Submitting job to CyteType...")
 
   tryCatch({
     # Validate inputs
@@ -69,8 +69,10 @@
   # Info for auth token uses
   if (!is.null(auth_token)) {
     log_info("Token secured report (updates automatically): \n{report_url}")
+    cli::cli_text("{.url {report_url}}")
   } else {
-    log_info("Report (updates automatically) available at: \n{report_url}")
+    log_info("Report (updates automatically) available at: \n")
+    cli::cli_text("{.url {report_url}}")
   }
 
   log_info("If disconnected, retrieve results with: GetResults()")

R/cytetype.R

@@ -59,7 +59,7 @@
 #' }
 #'
 #' @importFrom logger log_info log_debug log_error log_warn
-#' @importFrom dplyr group_by filter slice_head ungroup %>%
+#' @importFrom dplyr group_by filter slice_head ungroup arrange desc %>%
 #' @importFrom tidyr pivot_longer
 #' @importFrom stats setNames
 #' @importFrom Seurat Embeddings GetAssayData AddMetaData
@@ -95,12 +95,16 @@ PrepareCyteTypeR <- function(obj,
 
   marker_genes <- marker_table %>%
     group_by(cluster) %>%
-    dplyr::filter(avg_log2FC > 1) %>%
+    arrange(desc(avg_log2FC)) %>%
     slice_head(n = n_top_genes) %>%
     ungroup() %>%
     {split(.$gene, .$cluster)}
   names(marker_genes) <- cluster_map[names(marker_genes)]
 
+  if (any(sapply(marker_genes, function(x) !is.vector(x) || length(x) < 5))) {
+    stop("Invalid marker genes, some clusters have fewer than 5 markers")
+  }
+
   print("Preparing visualisation data...")
   visualization_data <- list(
     coordinates = Embeddings(obj, reduction = coordinates_key),
@@ -248,13 +252,12 @@ CyteTypeR <- function(obj,
 
 
   # Job submission
-  tryCatch({
-    job_id <- .submit_job(query_list, api_url, auth_token)
-    },
-    error = function(e) {
-      stop("Job submission failed: ", conditionMessage(e))
-    }
-  )
+
+  job_id <- .submit_job(query_list, api_url, auth_token)
+  if (is.na(job_id)) {
+    stop("Job submission failed.")
+  }
+
 
   # Save job details
   report_url <- file.path(api_url, 'report',job_id)