Did not find any barcode-spots of the specified object in input for 'feature_df'.

DESCRIPTION

@@ -3,16 +3,17 @@ Type: Package
 Title: A Toolbox for Spatial Gene Expression Analysis
 Version: 0.1.0
 Authors@R: as.person(c(
-    "Jan Kueckelhaus <jan.kueckelhaus@uniklinik-freiburg.de> [aut, cre]", 
+    "Jan Kueckelhaus <jan.kueckelhaus@uniklinik-freiburg.de> [aut, cre]",
     "Dieter-Henrik Heiland <dr.dieter.henrik.heiland@uniklinik-freiburg.de> [aut]"
   ))
-Description: This package provides a framework of functions and shiny-applications to make it as easy  and intuitive as possible to work with spatial gene expression data. 
+Description: This package provides a framework of functions and shiny-applications to make it as easy  and intuitive as possible to work with spatial gene expression data.
 Encoding: UTF-8
 LazyData: true
 License: GPL-3
 BugReports: themilolab-spata@gmx.de
-RoxygenNote: 7.1.1
-Imports: 
+RoxygenNote: 7.2.3
+Imports:
+    biomaRt,
     broom,
     concaveman,
     colorspace,
@@ -33,19 +34,23 @@ Imports:
     rlang,
     readr,
     reticulate,
+    Seurat,
     shiny,
     shinyWidgets,
     shinybusy,
     shinydashboard,
+    SingleCellExperiment,
     sp,
     stringr,
     stringi,
+    SummarizedExperiment,
     tibble,
     tidyr,
     tidytext,
     viridis,
     umap
-Collate: 
+Collate:
+    'GetPositions.R'
     'S4-documentation.R'
     'S4-generic-functions.R'
     'S4-programming-aid.R'
@@ -109,6 +114,6 @@ Collate:
     'update-spata-object.R'
     'valid-input-options.R'
     'validation.R'
-Depends: 
+Depends:
     R (>= 2.10)
 URL: https://themilolab.com/

R/GetPositions.R

@@ -0,0 +1,98 @@
+#' Remove alternative chromosomes, X chromosome, Y chromosome, and mitochondrial genome from a gene positions dataframe
+#'
+#' This function removes alternative chromosomes, X chromosome, Y chromosome, and mitochondrial genome from a gene positions dataframe.
+#' It also removes any duplicated genes, sorts the dataframe by chromosome column in numeric order, and returns the modified dataframe.
+#'
+#' @param gene_positions_df A data frame containing gene positions.
+#' @return A modified gene positions dataframe with alternative chromosomes, X chromosome, Y chromosome, and mitochondrial chromosome removed, sorted in numeric order.
+#' @examples
+#' gene_positions <- data.frame(
+#'   ensembl_gene_id = c("ENSG00000261846", "ENSG00000197953", "ENSG00000262466"),
+#'   hgnc_symbol = c("AADACL2", "AADACL2", "AADACL2-AS1"),
+#'   chromosome_name = c("CHR_HSCHR3_1_CTG2_1", "3", "CHR_HSCHR3_1_CTG2_1"),
+#'   start_position = c(151744454, 151733916, 151761981),
+#'   end_position = c(151770036, 151761339, 151765669)
+#' )
+#' ignoreAlternative(gene_positions)
+#'
+#' @export
+ignoreAlternative <- function(gene_positions_df) {
+
+    # Sort the dataframe by chromosome column
+    gene_positions_df <- gene_positions_df[order(gene_positions_df[, 3], decreasing = F), ]
+
+    # Remove duplicates based on the gene column
+    gene_positions_df <- gene_positions_df[!duplicated(gene_positions_df[, 2]), ]
+
+    # Replace alternative chromosome names with numeric codes
+    gene_positions_df[which(gene_positions_df[, 3] == "X"), 3] <- 23
+    gene_positions_df[which(gene_positions_df[, 3] == "Y"), 3] <- 24
+    gene_positions_df[which(gene_positions_df[, 3] == "MT"), 3] <- 0
+
+    # Remove any chromosome names that are longer than 2 characters
+    gene_positions_df[which(nchar(gene_positions_df[, 3]) > 2), 3] <- 0
+
+    # Sort the dataframe by chromosome column in numeric order
+    gene_positions_df <- gene_positions_df[order(as.numeric(gene_positions_df[, 3]), decreasing = F), ]
+
+    # Return the modified dataframe
+    return(gene_positions_df)
+}
+
+#' Receive genomic coordinates of a gene list
+#'
+#' This function allows to receive the genomic positions of a vector of genes in HUGO format.
+#' @param gene_names A vector of gene names in HUGO format.
+#' @param ensembl_version Version of the ENSEMBL database used to quantify gene expression data. Default: v109.
+#' @param ignoreAlt If set to TRUE: Ignore if multiple loci are reported for a gene, pick the one from the primary assembly.
+#' @keywords Chromosomal positions
+#' @export
+#' @examples
+#' getGenePositions(gene_names = c("EGFR", "PDGFRA"))
+getGenePositions <- function(gene_names = character(0),
+                             ensembl_version = "https://feb2023.archive.ensembl.org",
+                             species = "human",
+                             ignoreAlt = F) {
+    if (species == "human") {
+        ensembl <- biomaRt::useMart(
+            biomart = "ENSEMBL_MART_ENSEMBL",
+            dataset = "hsapiens_gene_ensembl",
+            host = ensembl_version # use biomaRt::listEnsemblArchives() to check the versions
+        )
+
+        if (length(gene_names) == 0) {
+            gene_names <- biomaRt::getBM(attributes = "hgnc_symbol", mart = ensembl)$hgnc_symbol
+        }
+
+        gene_positions <- biomaRt::getBM(
+            attributes = c("ensembl_gene_id", "hgnc_symbol", "chromosome_name", "start_position", "end_position"),
+            filters = "hgnc_symbol",
+            values = gene_names,
+            mart = ensembl
+        )
+    } else if (species == "mouse") {
+        ensembl <- biomaRt::useMart(
+            biomart = "ENSEMBL_MART_ENSEMBL",
+            dataset = "mmusculus_gene_ensembl",
+            host = ensembl_version # use biomaRt::listEnsemblArchives() to check the versions
+        )
+
+        if (length(gene_names) == 0) {
+            gene_names <- biomaRt::getBM(attributes = "mgi_symbol", mart = ensembl)$mgi_symbol
+        }
+
+        gene_positions <- biomaRt::getBM(
+            attributes = c("ensembl_gene_id", "mgi_symbol", "chromosome_name", "start_position", "end_position"),
+            filters = "mgi_symbol",
+            values = gene_names,
+            mart = ensembl
+        )
+    } else {
+        stop("Species other than human and mouse are not supported.")
+    }
+
+    if (ignoreAlt == T) {
+        gene_positions <- ignoreAlternative(gene_positions)
+    }
+    return(gene_positions)
+}

R/cnv-analysis.R

@@ -167,11 +167,17 @@ hlpr_run_cnva_pca <- function(object, n_pcs = 30, of_sample = NA, ...){
 #' character variables \emph{ensembl_gene_id}, \emph{hgnc_symbol}, \emph{chromosome_name}
 #' and two numeric variables \emph{start_position} and \emph{end_position.}.
 #'
-#' If NULL the data.frame is created via \code{CONICsmat::getGenePositions()} using
-#' all gene names that appear in the count matrix and in the reference matrix.
+#' If NULL, the data.frame is created via custom function \code{getGenePositions()}
+#' adapted from \code{CONICsmat::getGenePositions()}
+#' using #' all gene names that retrieved from ensembl.
 #'
 #' Defaults to the SPATA2 intern data.frame \code{SPATA2::gene_pos_df}.
 #'
+#' @param remove_alternative_chr either TRUE or FALSE.
+#' If TRUE, remove the chromosome of 0 (mitochondria and contigs), 23 (X), and 24 (Y).
+#' If FALSE, keep the chromosome of 0 (mitochondria and contigs), 23 (X), and 24 (Y).
+#' Defaults to TRUE to reduce confusion of the user.
+#'
 #' @param cnv_prefix Character value. Denotes the string with which the
 #' the feature variables in which the information about the chromosomal gains and
 #' losses are stored are prefixed.
@@ -253,6 +259,7 @@ runCnvAnalysis <- function(object,
                            ref_mtr = cnv_ref[["mtr"]], # reference data set of healthy tissue
                            ref_regions = cnv_ref[["regions"]], # chromosome positions
                            gene_pos_df = SPATA2::gene_pos_df,
+                           remove_alternative_chr = TRUE,
                            directory_cnv_folder = "data-development/cnv-results", # output folder
                            directory_regions_df = NA, # deprecated (chromosome positions)
                            n_pcs = 30,
@@ -401,28 +408,43 @@ runCnvAnalysis <- function(object,
 
   }
 
-  if(base::is.data.frame(gene_pos_df)){
+  if (base::is.data.frame(gene_pos_df)){
+    base::message(
+      "Default or user-provided dataframe is used."
+    )
 
-    confuns::check_data_frame(
-      df = gene_pos_df,
-      var.class = list(
-        ensembl_gene_id = "character",
-        hgnc_symbol = "character",
-        chromosome_name = "character",
-        start_position = "integer",
-        end_position = "integer"
-      )
+  } else if (base::is.null(gene_pos_df)){
+    base::message(
+      "The function getGenePositions() will be use to extract the gene position dataframe."
     )
 
+    # custom getGenePositions() is adapted from CONICSmat::getGenePositions()
+    gene_pos_df <- getGenePositions(ignoreAlt = T)
+    # usethis::use_data(gene_pos_df, overwrite = T) # how to make the built-in rda.
 
   } else {
+    base::stop("No other options for gene position dataframe.")
+  }
 
-    gene_pos_df <-
-      CONICSmat::getGenePositions(gene_names = base::rownames(expr_inter))
+  # Validate the column type of the gene_pos_df.
+  confuns::check_data_frame(
+    df = gene_pos_df,
+    var.class = list(
+      ensembl_gene_id = "character",
+      hgnc_symbol = "character",
+      chromosome_name = "character",
+      start_position = "integer",
+      end_position = "integer"
+    )
+  )
 
+  # Remove the chromosome of 0 (mitochondria and contigs), 23 (X), and 24 (Y)
+  if (remove_alternative_chr == TRUE) {
+    gene_pos_df <- dplyr::filter(gene_pos_df, !(chromosome_name %in% c("0", "23", "24")))
   }
 
 
+
   # -----
 
 
@@ -687,7 +709,7 @@ runCnvAnalysis <- function(object,
   result_dir <-
     stringr::str_c(directory_cnv_folder, "/", plot_cnv$output_filename, ".observations.txt")
 
-  results <- utils::read.table(result_dir)
+  results <- utils::read.table(result_dir, check.names = FALSE)
 
   bcs_object <-
     getFeatureDf(object) %>%
@@ -724,7 +746,6 @@ runCnvAnalysis <- function(object,
     base::as.data.frame() %>%
     tibble::rownames_to_column(var = "barcodes") %>%
     magrittr::set_colnames(value = cnames) %>%
-    dplyr::mutate(barcodes = stringr::str_replace_all(string = barcodes, pattern = "\\.", replacement = "-")) %>%
     dplyr::mutate(dplyr::across(dplyr::starts_with(match = cnv_prefix), .fns = base::as.numeric)) %>%
     tibble::as_tibble()
 
@@ -740,13 +761,6 @@ runCnvAnalysis <- function(object,
       )
 
   # cnv matrix
-  base::colnames(results) <-
-    stringr::str_replace_all(
-      string = base::colnames(results),
-      pattern = "\\.",
-      replacement = "-"
-      )
-
   cnv_mtr <- base::as.matrix(results)
 
   # cnv list