pull main to dev

.gitignore

@@ -3,4 +3,4 @@
 .RData
 .Ruserdata
 inst/doc
-docs
+docs/

R/decide_ReSegment_Operations.R

@@ -434,30 +434,3 @@ check_config_leiden <- function(config){
 
   return(config)
 }
-
-#' @title run_igraph_leiden
-#' @description Run Leiden clustering with version-compatible resolution argument.
-#' @param graph An igraph object representing the graph to cluster.
-#' @param ... Additional arguments passed to `cluster_leiden()`, such as
-#'   `objective_function`, `resolution_parameter`, `beta`, `initial_membership`,
-#'   and `n_iterations`.
-#' @return A clustering object returned by `cluster_leiden()`.
-#' @details This function wraps `igraph::cluster_leiden()` and ensures compatibility
-#' with both older (<2.1.0) and newer versions of the `igraph` package by renaming
-#' the `resolution_parameter` argument to `resolution` if needed.
-#' @importFrom igraph cluster_leiden
-run_igraph_leiden <- function(graph, ...) {
-  args <- list(...)
-
-  # Rename resolution_parameter to resolution if igraph >= 2.1.0
-  if (packageVersion("igraph") >= "2.1.0") {
-    if ("resolution_parameter" %in% names(args)) {
-      args$resolution <- args$resolution_parameter
-      args$resolution_parameter <- NULL
-    }
-  }
-
-  # Call cluster_leiden with modified arguments
-  do.call(igraph::cluster_leiden, c(list(graph), args))
-}
-

R/file_utilities.R

@@ -29,10 +29,7 @@ myFun_fov_load <- function(path_to_fov) {
   } else if (grepl("\\.csv$", base_path, ignore.case = TRUE)) {
     con <- if (is_gz) gzfile(path_to_fov) else path_to_fov
     each_transDF <- read.csv(con, sep = ',', header = TRUE)
-  } else if (grepl("\\.txt$", base_path, ignore.case = TRUE)) {
-    con <- if (is_gz) gzfile(path_to_fov) else path_to_fov
-    each_transDF <- read.csv(con, sep = '\t', header = TRUE)
-  } else if (grepl("\\.tsv$", base_path, ignore.case = TRUE)) {
+  } else if (grepl("\\.txt$|\\.tsv$", base_path, ignore.case = TRUE)) {
     con <- if (is_gz) gzfile(path_to_fov) else path_to_fov
     each_transDF <- read.csv(con, sep = '\t', header = TRUE)
   } else {
@@ -138,7 +135,7 @@ prepare_perFOV_transDF <- function(each_transDF,
   raw_locs <- each_transDF[, orig_spatLocs_colns]
 
   # flip y coordinates (2nd) to have images shown from top to bottom
-  if(invert_y){
+  if(invert_y==TRUE){
     raw_locs[[orig_spatLocs_colns[2]]] <- 0-raw_locs[[orig_spatLocs_colns[2]]]
   }
 

R/group_transcripts_in_space.R

@@ -493,19 +493,3 @@ myFun_3point_singleCell <- function(dfCoord_subset,
 }
 
 
-#' @title igraph_delete_edges
-#' @description Delete edges from an igraph object with version compatibility
-#' @param graph An igraph object from which edges will be deleted.
-#' @param edges A vector of edge IDs or an edge selector to delete.
-#'
-#' @return An igraph object with the specified edges removed.
-#' @details This function wraps `igraph::delete_edges()` and ensures compatibility
-#' with older versions (<2.0.0) of `igraph` that used `delete.edges()`.
-igraph_delete_edges <- function(graph, edges) {
-  if (packageVersion("igraph") >= "2.0.0") {
-    igraph::delete_edges(graph, edges)
-  } else {
-    igraph::delete.edges(graph, edges)
-  }
-}
-

R/other_utilities.R

@@ -0,0 +1,43 @@
+#' @title run_igraph_leiden
+#' @description Run Leiden clustering with version-compatible resolution argument.
+#' @param graph An igraph object representing the graph to cluster.
+#' @param ... Additional arguments passed to `cluster_leiden()`, such as
+#'   `objective_function`, `resolution_parameter`, `beta`, `initial_membership`,
+#'   and `n_iterations`.
+#' @return A clustering object returned by `cluster_leiden()`.
+#' @details This function wraps `igraph::cluster_leiden()` and ensures compatibility
+#' with both older (<2.1.0) and newer versions of the `igraph` package by renaming
+#' the `resolution_parameter` argument to `resolution` if needed.
+#' @importFrom igraph cluster_leiden
+run_igraph_leiden <- function(graph, ...) {
+  args <- list(...)
+
+  # Rename resolution_parameter to resolution if igraph >= 2.1.0
+  if (packageVersion("igraph") >= "2.1.0") {
+    if ("resolution_parameter" %in% names(args)) {
+      args$resolution <- args$resolution_parameter
+      args$resolution_parameter <- NULL
+    }
+  }
+
+  # Call cluster_leiden with modified arguments
+  do.call(igraph::cluster_leiden, c(list(graph), args))
+}
+
+
+#' @title igraph_delete_edges
+#' @description Delete edges from an igraph object with version compatibility
+#' @param graph An igraph object from which edges will be deleted.
+#' @param edges A vector of edge IDs or an edge selector to delete.
+#'
+#' @return An igraph object with the specified edges removed.
+#' @details This function wraps `igraph::delete_edges()` and ensures compatibility
+#' with older versions (<2.0.0) of `igraph` that used `delete.edges()`.
+igraph_delete_edges <- function(graph, edges) {
+  if (packageVersion("igraph") >= "2.0.0") {
+    igraph::delete_edges(graph, edges)
+  } else {
+    igraph::delete.edges(graph, edges)
+  }
+}
+

README.md

@@ -1,9 +1,9 @@
 # FastReseg
  An R package for detection and correction of cell segmentation error based on spatial profile of transcripts
 
-#### [Manuscript](https://www.biorxiv.org/content/10.1101/2024.12.05.627051v1.abstract):
+#### [Manuscript](https://www.nature.com/articles/s41598-025-08733-5):
 
-Wu L, Beechem JM, Danaher P. FastReseg: using transcript locations to refine image-based cell segmentation results in spatial transcriptomics. *bioRxiv* 2024.12.05.627051; doi: https://doi.org/10.1101/2024.12.05.627051
+Wu, L., Beechem, J.M. & Danaher, P. Using transcripts to refine image based cell segmentation with FastReseg. Sci Rep 15, 30508 (2025). https://doi.org/10.1038/s41598-025-08733-5
 
 ### Dev notes 
 `FastReseg` package processes spatial transcriptome data through 5 different modules: 

_pkgdown.yml

@@ -112,7 +112,7 @@ external-articles:
   title: Working principles and Manuscript
   description: Manuscript for FastReseg describing working principles, performance
     characterization and parameter impacts.
-  href: https://www.biorxiv.org/content/10.1101/2024.12.05.627051v1.abstract
+  href: https://www.nature.com/articles/s41598-025-08733-5
 
 articles:
 - title: Manuscript