update

Author: junjunlab

NAMESPACE

@@ -61,6 +61,7 @@ export(subset_data)
 export(theme_ribo)
 export(to_position_matrix)
 export(trans_plot)
+export(trans_plot2)
 export(vocalno_plot)
 export(whole_metagene_plot)
 exportClasses(ribotrans)
@@ -96,6 +97,7 @@ exportMethods(relative_motif_occupancy)
 exportMethods(relative_offset_plot)
 exportMethods(subset_data)
 exportMethods(trans_plot)
+exportMethods(trans_plot2)
 exportMethods(whole_metagene_plot)
 import(Rcpp)
 import(RcppArmadillo)

R/serp-visualization.R

@@ -763,22 +763,6 @@ setMethod("enrichment_plot2",
 # ==============================================================================
 
 
-#' Plot translation profiles
-#'
-#' @description
-#' This is a generic function for plotting translation-related profiles (such as
-#' ribosome occupancy or enrichment signals) for different types of transcriptome data.
-#'
-#' @param object An object of class \code{serp} or \code{ribotrans}, containing necessary data for plotting.
-#' @param ... Additional arguments passed to the specific method.
-#'
-#' @return A plot, typically a ggplot2 object.
-#'
-#' @export
-setGeneric("trans_plot",function(object,...) standardGeneric("trans_plot"))
-
-
-
 
 #' Plot Ribosome density Across Transcripts
 #'
@@ -805,6 +789,7 @@ setGeneric("trans_plot",function(object,...) standardGeneric("trans_plot"))
 #' @param nrow Number of rows in the final layout when multiple transcripts are plotted. Passed to \code{cowplot::plot_grid()}.
 #' @param ncol Number of columns in the final layout when multiple transcripts are plotted. Passed to \code{cowplot::plot_grid()}.
 #' @param return_data Logical. If \code{TRUE}, return the underlying processed data instead of plot. Default: \code{FALSE}.
+#' @param ... Additional arguments (currently unused).
 #'
 #'
 #' @details
@@ -832,16 +817,22 @@ setGeneric("trans_plot",function(object,...) standardGeneric("trans_plot"))
 #' @examples
 #' \dontrun{
 #' # Plot ribosome and total signal at codon resolution
-#' trans_plot(serp_obj, mode = "codon")
+#' trans_plot2(serp_obj, mode = "codon")
 #'
 #' # Merge replicates and plot with standard deviation shading
-#' trans_plot(serp_obj, merge_rep = TRUE)
+#' trans_plot2(serp_obj, merge_rep = TRUE)
 #'
 #' # Return processed data without plotting
-#' data <- trans_plot(serp_obj, return_data = TRUE)
+#' data <- trans_plot2(serp_obj, return_data = TRUE)
 #' }
 #' @export
-setMethod("trans_plot",
+setGeneric("trans_plot2",function(object,...) standardGeneric("trans_plot2"))
+
+
+
+#' @rdname trans_plot2
+#' @export
+setMethod("trans_plot2",
           signature(object = "serp"),
           function(object,
                    merge_rep = FALSE,

R/visualization-methods.R

@@ -2,7 +2,6 @@
 # visualization
 # ==============================================================================
 
-
 #' Plot RNA-seq and Ribosome Occupancy along Transcripts
 #'
 #' @description
@@ -30,6 +29,8 @@
 #' @param cds_col Colors used to annotate CDS in \code{ggside} alignment strip. Default: \code{"grey30"}.
 #' @param nrow Number of rows in the final layout when multiple transcripts are plotted. Passed to \code{cowplot::plot_grid()}.
 #' @param ncol Number of columns in the final layout when multiple transcripts are plotted. Passed to \code{cowplot::plot_grid()}.
+#' @param ... Additional arguments (currently unused).
+#'
 #'
 #' @details
 #' This method supports four types of data display:
@@ -67,6 +68,12 @@
 #' }
 #'
 #' @export
+setGeneric("trans_plot",function(object,...) standardGeneric("trans_plot"))
+
+
+
+#' @rdname trans_plot
+#' @export
 setMethod("trans_plot",
           signature(object = "ribotrans"),
           function(object,