@@ -69,7 +69,7 @@ plot_region_impl <- function(

             mod_scale = mod_scale

         ) +

         ggplot2::coord_cartesian(xlim = xlim, expand = FALSE) +

-        ggplot2::labs(x = "Position", y = "Mean Methylation Probability")

+        ggplot2::labs(x = "Position", y = "Mean Modification Probability")

     p_out <- p1

@@ -126,13 +126,16 @@ plot_region_impl <- function(

 #' @param span DEPRECATED, use smoothing_window instead. Will be removed in next version.

 #'

 #' @details

-#' This function plots the methylation data for a given region. The region is specified by

-#' chromosome, start and end positions. The basic plot contains a smoothed line plot of

-#' the methylation of each experimental group. Since V3.0.0 NanoMethViz has changed the

-#' smoothing strategy from a loess smoothing to a weighted moving average. This is because

-#' the loess smoothing was too computationally expensive for large datasets and had a

-#' span parameter that was difficult to tune. The new smoothing strategy is controlled

-#' by the smoothing_window argument.

+#' This function plots the methylation data for a given region. The main trendline plot shows the average methylation

+#' probability across the region. The heatmap plot shows the methylation probability for each read across the region.

+#' The gene annotation plot shows the exons of the region. In the heatmap, each row represents one or more

+#' non-overlapping reads where the coloured segments represent the methylation probability at each position. Data along

+#' a read is connected by a grey line. The gene annotation plot shows the isoforms and exons of genes within the region,

+#' with arrows indicating the direction of transcription.

+#'

+#' Since V3.0.0 NanoMethViz has changed the smoothing strategy from a loess smoothing to a weighted moving average. This

+#' is because the loess smoothing was too computationally expensive for large datasets and had a span parameter that was

+#' difficult to tune. The new smoothing strategy is controlled by the smoothing_window argument.

 #'

 #' @examples

 #' nmr <- load_example_nanomethresult()

@@ -53,25 +53,23 @@ plot_region_impl <- function(

     title <- glue::glue("{chr}:{start}-{end}")

     xlim <- round(c(start - window_left, end + window_right))

     p1 <- plot_methylation_data(

-        methy_data = methy_data,

-        start = start,

-        end = end,

-        chr = chr,

-        title = title,

-        anno_regions = anno_regions,

-        binary_threshold = binary_threshold,

-        avg_method = avg_method,

-        spaghetti = spaghetti,

-        sample_anno = sample_anno,

-        smoothing_window = smoothing_window,

-        palette_col = palette,

-        line_size = line_size,

-        mod_scale = mod_scale

-    ) +

-        ggplot2::coord_cartesian(

-            xlim = xlim,

-            expand = FALSE

-        )

+            methy_data = methy_data,

+            start = start,

+            end = end,

+            chr = chr,

+            title = title,

+            anno_regions = anno_regions,

+            binary_threshold = binary_threshold,

+            avg_method = avg_method,

+            spaghetti = spaghetti,

+            sample_anno = sample_anno,

+            smoothing_window = smoothing_window,

+            palette_col = palette,

+            line_size = line_size,

+            mod_scale = mod_scale

+        ) +

+        ggplot2::coord_cartesian(xlim = xlim, expand = FALSE) +

+        ggplot2::labs(x = "Position", y = "Mean Methylation Probability")

     p_out <- p1

@@ -1,211 +1,4 @@

-#' @rdname plot_region

-#'

-#' @param anno_regions the data.frame of regions to be annotated.

-#' @param binary_threshold the modification probability such that calls with

-#'   modification probability above the threshold are set to 1 and probabilities

-#'   equal to or below the threshold are set to 0.

-#' @param avg_method the average method for pre-smoothing at each genomic position.

-#'   Data is pre-smoothed at each genomic position before the smoothed aggregate line

-#'   is generated for performance reasons. The default is "mean" which corresponds

-#'   to the average methylation fraction. The alternative "median" option is

-#'   closer to an average within the more common methylation state.

-#' @param spaghetti whether or not individual reads should be shown.

-#' @param heatmap whether or not read-methylation heatmap should be shown.

-#' @param heatmap_subsample how many packed rows of reads to subsample to.

-#' @param smoothing_window the window size for smoothing the trend line.

-#' @param window_prop the size of flanking region to plot. Can be a vector of two

-#'   values for left and right window size. Values indicate proportion of gene

-#'   length.

-#' @param palette the ggplot colour palette used for groups.

-#' @param line_size the size of the lines.

-#' @param mod_scale the scale range for modification probabilities. Default c(0, 1), set to "auto" for automatic

-#'   limits.

-#' @param span DEPRECATED, use smoothing_window instead. Will be removed in next version.

-#'

-#' @details

-#' This function plots the methylation data for a given region. The region is specified by

-#' chromosome, start and end positions. The basic plot contains a smoothed line plot of

-#' the methylation of each experimental group. Since V3.0.0 NanoMethViz has changed the

-#' smoothing strategy from a loess smoothing to a weighted moving average. This is because

-#' the loess smoothing was too computationally expensive for large datasets and had a

-#' span parameter that was difficult to tune. The new smoothing strategy is controlled

-#' by the smoothing_window argument.

-#'

-#' @examples

-#' nmr <- load_example_nanomethresult()

-#' plot_region(nmr, "chr7", 6703892, 6730431)

-#'

-#' @export

-setMethod("plot_region",

-    signature(

-        x = "NanoMethResult",

-        chr = "character",

-        start = "numeric",

-        end = "numeric"),

-

-    function(

-        x,

-        chr,

-        start,

-        end,

-        anno_regions = NULL,

-        binary_threshold = NULL,

-        avg_method = c("mean", "median"),

-        spaghetti = FALSE,

-        heatmap = FALSE,

-        heatmap_subsample = 50,

-        smoothing_window = 2000,

-        gene_anno = TRUE,

-        window_prop = 0,

-        palette = ggplot2::scale_colour_brewer(palette = "Set1"),

-        line_size = 1,

-        mod_scale = c(0, 1),

-        span = NULL

-    ) {

-        if (!missing("span")) {

-            warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

-        }

-        avg_method <- match.arg(avg_method)

-

-        plot_region_impl(

-            x = x,

-            chr = chr,

-            start = start,

-            end = end,

-            anno_regions = anno_regions,

-            binary_threshold = binary_threshold,

-            avg_method = avg_method,

-            spaghetti = spaghetti,

-            heatmap = heatmap,

-            heatmap_subsample = heatmap_subsample,

-            smoothing_window = smoothing_window,

-            gene_anno = gene_anno,

-            window_prop = window_prop,

-            palette = palette,

-            line_size = line_size,

-            mod_scale = mod_scale

-        )

-    }

-)

-

-#' @rdname plot_region

-#' @export

-setMethod("plot_region",

-    signature(

-        x = "ModBamResult",

-        chr = "character",

-        start = "numeric",

-        end = "numeric"),

-

-    function(

-        x,

-        chr,

-        start,

-        end,

-        anno_regions = NULL,

-        binary_threshold = NULL,

-        avg_method = c("mean", "median"),

-        spaghetti = FALSE,

-        heatmap = FALSE,

-        heatmap_subsample = 50,

-        smoothing_window = 2000,

-        gene_anno = TRUE,

-        window_prop = 0,

-        palette = ggplot2::scale_colour_brewer(palette = "Set1"),

-        line_size = 1,

-        mod_scale = c(0, 1),

-        span = NULL

-    ) {

-        if (!missing("span")) {

-            warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

-        }

-        avg_method <- match.arg(avg_method)

-

-        plot_region_impl(

-            x = x,

-            chr = chr,

-            start = start,

-            end = end,

-            anno_regions = anno_regions,

-            binary_threshold = binary_threshold,

-            avg_method = avg_method,

-            spaghetti = spaghetti,

-            heatmap = heatmap,

-            heatmap_subsample = heatmap_subsample,

-            smoothing_window = smoothing_window,

-            gene_anno = gene_anno,

-            window_prop = window_prop,

-            palette = palette,

-            line_size = line_size,

-            mod_scale = mod_scale

-        )

-    }

-)

-

-#' @rdname plot_region

-#' @export

-setMethod("plot_region",

-    signature(

-        x = "NanoMethResult",

-        chr = "factor",

-        start = "numeric",

-        end = "numeric"),

-

-    function(

-        x,

-        chr,

-        start,

-        end,

-        anno_regions = NULL,

-        binary_threshold = NULL,

-        avg_method = c("mean", "median"),

-        spaghetti = FALSE,

-        heatmap = FALSE,

-        heatmap_subsample = 50,

-        smoothing_window = 2000,

-        gene_anno = TRUE,

-        window_prop = 0,

-        palette = ggplot2::scale_colour_brewer(palette = "Set1"),

-        line_size = 1,

-        mod_scale = c(0, 1),

-        span = NULL

-    ) {

-        if (!missing("span")) {

-            warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

-        }

-        avg_method <- match.arg(avg_method)

-

-        plot_region_impl(

-            x = x,

-            chr = chr,

-            start = start,

-            end = end,

-            anno_regions = anno_regions,

-            binary_threshold = binary_threshold,

-            avg_method = avg_method,

-            spaghetti = spaghetti,

-            heatmap = heatmap,

-            heatmap_subsample = heatmap_subsample,

-            smoothing_window = smoothing_window,

-            gene_anno = gene_anno,

-            window_prop = window_prop,

-            palette = palette,

-            line_size = line_size,

-            mod_scale = mod_scale

-        )

-    }

-)

-

-#' @rdname plot_region

-#' @export

-setMethod("plot_region",

-    signature(

-        x = "ModBamResult",

-        chr = "factor",

-        start = "numeric",

-        end = "numeric"),

-

-    function(

+plot_region_impl <- function(

         x,

         chr,

         start,

@@ -214,7 +7,7 @@ setMethod("plot_region",

         binary_threshold = NULL,

         avg_method = c("mean", "median"),

         spaghetti = FALSE,

-        heatmap = FALSE,

+        heatmap = TRUE,

         heatmap_subsample = 50,

         smoothing_window = 2000,

         gene_anno = TRUE,

@@ -223,50 +16,6 @@ setMethod("plot_region",

         line_size = 1,

         mod_scale = c(0, 1),

         span = NULL

-    ) {

-        if (!missing("span")) {

-            warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

-        }

-        avg_method <- match.arg(avg_method)

-

-        plot_region_impl(

-            x = x,

-            chr = chr,

-            start = start,

-            end = end,

-            anno_regions = anno_regions,

-            binary_threshold = binary_threshold,

-            avg_method = avg_method,

-            spaghetti = spaghetti,

-            heatmap = heatmap,

-            heatmap_subsample = heatmap_subsample,

-            smoothing_window = smoothing_window,

-            gene_anno = gene_anno,

-            window_prop = window_prop,

-            palette = palette,

-            line_size = line_size,

-            mod_scale = mod_scale

-        )

-    }

-)

-

-plot_region_impl <- function(

-    x,

-    chr,

-    start,

-    end,

-    anno_regions,

-    binary_threshold,

-    avg_method,

-    spaghetti,

-    heatmap,

-    heatmap_subsample,

-    smoothing_window,

-    gene_anno,

-    window_prop,

-    palette,

-    line_size,

-    mod_scale

 ) {

     sample_anno <- samples(x)

     chr <- as.character(chr)

@@ -352,3 +101,68 @@ plot_region_impl <- function(

     p_out

 }

+

+#' @rdname plot_region

+#'

+#' @param anno_regions the data.frame of regions to be annotated.

+#' @param binary_threshold the modification probability such that calls with

+#'   modification probability above the threshold are set to 1 and probabilities

+#'   equal to or below the threshold are set to 0.

+#' @param avg_method the average method for pre-smoothing at each genomic position.

+#'   Data is pre-smoothed at each genomic position before the smoothed aggregate line

+#'   is generated for performance reasons. The default is "mean" which corresponds

+#'   to the average methylation fraction. The alternative "median" option is

+#'   closer to an average within the more common methylation state.

+#' @param spaghetti whether or not individual reads should be shown.

+#' @param heatmap whether or not read-methylation heatmap should be shown.

+#' @param heatmap_subsample how many packed rows of reads to subsample to.

+#' @param smoothing_window the window size for smoothing the trend line.

+#' @param gene_anno whether to show gene annotation.

+#' @param window_prop the size of flanking region to plot. Can be a vector of two

+#'   values for left and right window size. Values indicate proportion of gene

+#'   length.

+#' @param palette the ggplot colour palette used for groups.

+#' @param line_size the size of the lines.

+#' @param mod_scale the scale range for modification probabilities. Default c(0, 1), set to "auto" for automatic

+#'   limits.

+#' @param span DEPRECATED, use smoothing_window instead. Will be removed in next version.

+#'

+#' @details

+#' This function plots the methylation data for a given region. The region is specified by

+#' chromosome, start and end positions. The basic plot contains a smoothed line plot of

+#' the methylation of each experimental group. Since V3.0.0 NanoMethViz has changed the

+#' smoothing strategy from a loess smoothing to a weighted moving average. This is because

+#' the loess smoothing was too computationally expensive for large datasets and had a

+#' span parameter that was difficult to tune. The new smoothing strategy is controlled

+#' by the smoothing_window argument.

+#'

+#' @examples

+#' nmr <- load_example_nanomethresult()

+#' plot_region(nmr, "chr7", 6703892, 6730431)

+#'

+#' @export

+setMethod("plot_region",

+    signature(x = "NanoMethResult", chr = "character", start = "numeric", end = "numeric"),

+    plot_region_impl

+)

+

+#' @rdname plot_region

+#' @export

+setMethod("plot_region",

+    signature(x = "ModBamResult", chr = "character", start = "numeric", end = "numeric"),

+    plot_region_impl

+)

+

+#' @rdname plot_region

+#' @export

+setMethod("plot_region",

+    signature(x = "NanoMethResult", chr = "factor", start = "numeric", end = "numeric"),

+    plot_region_impl

+)

+

+#' @rdname plot_region

+#' @export

+setMethod("plot_region",

+    signature(x = "ModBamResult", chr = "factor", start = "numeric", end = "numeric"),

+    plot_region_impl

+)

@@ -42,6 +42,7 @@ setMethod("plot_region",

         chr = "character",

         start = "numeric",

         end = "numeric"),

+

     function(

         x,

         chr,

@@ -54,6 +55,7 @@ setMethod("plot_region",

         heatmap = FALSE,

         heatmap_subsample = 50,

         smoothing_window = 2000,

+        gene_anno = TRUE,

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

@@ -72,11 +74,12 @@ setMethod("plot_region",

             end = end,

             anno_regions = anno_regions,

             binary_threshold = binary_threshold,

-            spaghetti = spaghetti,

             avg_method = avg_method,

+            spaghetti = spaghetti,

             heatmap = heatmap,

             heatmap_subsample = heatmap_subsample,

             smoothing_window = smoothing_window,

+            gene_anno = gene_anno,

             window_prop = window_prop,

             palette = palette,

             line_size = line_size,

@@ -93,6 +96,7 @@ setMethod("plot_region",

         chr = "character",

         start = "numeric",

         end = "numeric"),

+

     function(

         x,

         chr,

@@ -105,6 +109,7 @@ setMethod("plot_region",

         heatmap = FALSE,

         heatmap_subsample = 50,

         smoothing_window = 2000,

+        gene_anno = TRUE,

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

@@ -123,11 +128,12 @@ setMethod("plot_region",

             end = end,

             anno_regions = anno_regions,

             binary_threshold = binary_threshold,

-            spaghetti = spaghetti,

             avg_method = avg_method,

+            spaghetti = spaghetti,

             heatmap = heatmap,

             heatmap_subsample = heatmap_subsample,

             smoothing_window = smoothing_window,

+            gene_anno = gene_anno,

             window_prop = window_prop,

             palette = palette,

             line_size = line_size,

@@ -157,6 +163,7 @@ setMethod("plot_region",

         heatmap = FALSE,

         heatmap_subsample = 50,

         smoothing_window = 2000,

+        gene_anno = TRUE,

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

@@ -166,9 +173,9 @@ setMethod("plot_region",

         if (!missing("span")) {

             warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

         }

-        chr <- as.character(chr)

         avg_method <- match.arg(avg_method)

-        plot_region(

+

+        plot_region_impl(

             x = x,

             chr = chr,

             start = start,

@@ -180,6 +187,7 @@ setMethod("plot_region",

             heatmap = heatmap,

             heatmap_subsample = heatmap_subsample,

             smoothing_window = smoothing_window,

+            gene_anno = gene_anno,

             window_prop = window_prop,

             palette = palette,

             line_size = line_size,

@@ -209,6 +217,7 @@ setMethod("plot_region",

         heatmap = FALSE,

         heatmap_subsample = 50,

         smoothing_window = 2000,

+        gene_anno = TRUE,

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

@@ -218,9 +227,9 @@ setMethod("plot_region",

         if (!missing("span")) {

             warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

         }

-        chr <- as.character(chr)

         avg_method <- match.arg(avg_method)

-        plot_region(

+

+        plot_region_impl(

             x = x,

             chr = chr,

             start = start,

@@ -232,6 +241,7 @@ setMethod("plot_region",

             heatmap = heatmap,

             heatmap_subsample = heatmap_subsample,

             smoothing_window = smoothing_window,

+            gene_anno = gene_anno,

             window_prop = window_prop,

             palette = palette,

             line_size = line_size,

@@ -252,12 +262,16 @@ plot_region_impl <- function(

     heatmap,

     heatmap_subsample,

     smoothing_window,

+    gene_anno,

     window_prop,

     palette,

     line_size,

     mod_scale

 ) {

     sample_anno <- samples(x)

+    chr <- as.character(chr)

+    start <- as.numeric(start)

+    end <- as.numeric(end)

     if (length(window_prop) == 1) {

         window_prop <- c(window_prop, window_prop)

@@ -313,8 +327,8 @@ plot_region_impl <- function(

     p_out <- p1

     # if exon anno exists, append it to plot

-    if (nrow(exons(x)) != 0) {

-        exons_anno <- query_exons_region(exons(x), chr = chr, start = start, end = end)

+    if (gene_anno && nrow(exons(x)) != 0) {

+        exons_anno <- query_exons_region(x, chr = chr, start = start, end = end)

         p2 <- plot_gene_annotation(exons_anno, xlim[1], xlim[2]) +

             ggplot2::coord_cartesian(xlim = xlim, expand = FALSE) +

@@ -53,7 +53,7 @@ setMethod("plot_region",

         spaghetti = FALSE,

         heatmap = FALSE,

         heatmap_subsample = 50,

-        smoothing_window = 500,

+        smoothing_window = 2000,

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

@@ -104,7 +104,7 @@ setMethod("plot_region",

         spaghetti = FALSE,

         heatmap = FALSE,

         heatmap_subsample = 50,

-        smoothing_window = 500,

+        smoothing_window = 2000,

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

@@ -156,7 +156,7 @@ setMethod("plot_region",

         spaghetti = FALSE,

         heatmap = FALSE,

         heatmap_subsample = 50,

-        smoothing_window = 500,

+        smoothing_window = 2000,

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

@@ -208,7 +208,7 @@ setMethod("plot_region",

         spaghetti = FALSE,

         heatmap = FALSE,

         heatmap_subsample = 50,

-        smoothing_window = 500,

+        smoothing_window = 2000,

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

@@ -267,16 +267,17 @@ plot_region_impl <- function(

     window_left <- feature_width * window_prop[1]

     window_right <- feature_width * window_prop[2]

-    methy_data <-

-        query_methy(

-            x,

-            chr,

-            floor(start - window_left * 1.1),

-            ceiling(end + window_right * 1.1),

-            simplify = TRUE)

+    # query data

+    methy_data <- query_methy(

+        x,

+        chr,

+        floor(start - window_left * 1.1),

+        ceiling(end + window_right * 1.1),

+        simplify = TRUE

+    )

     if (nrow(methy_data) == 0) {

-        warning("no methylation data in region")

+        warning("no methylation data in region, returning empty plot")

         return(ggplot() + theme_void())

     }

@@ -284,6 +285,8 @@ plot_region_impl <- function(

         dplyr::select(-"strand") %>%

         tibble::as_tibble()

+

+    # setup base plot

     title <- glue::glue("{chr}:{start}-{end}")

     xlim <- round(c(start - window_left, end + window_right))

     p1 <- plot_methylation_data(

@@ -309,35 +312,27 @@ plot_region_impl <- function(

     p_out <- p1

-    # if exon anno exists

+    # if exon anno exists, append it to plot

     if (nrow(exons(x)) != 0) {

-        exons_anno <- query_exons_region(

-            exons(x),

-            chr = chr,

-            start = start,

-            end = end

-        )

+        exons_anno <- query_exons_region(exons(x), chr = chr, start = start, end = end)

         p2 <- plot_gene_annotation(exons_anno, xlim[1], xlim[2]) +

-            ggplot2::coord_cartesian(

-                xlim = xlim,

-                expand = FALSE

-            ) +

-                ggplot2::scale_x_continuous(labels = scales::label_number(scale_cut = scales::cut_si("b")))

-        anno_height <- attr(p2, "plot_height")

+            ggplot2::coord_cartesian(xlim = xlim, expand = FALSE) +

+            ggplot2::scale_x_continuous(labels = scales::label_number(scale_cut = scales::cut_si("b")))

+        anno_height <- attr(p2, "plot_height")

         heights <- c(1, 0.075 * anno_height)

+

         p_out <- p1 / p2 + patchwork::plot_layout(heights = heights)

     }

-    # if heatmap requested

+    # if heatmap requested, append it to plot

     if (heatmap) {

         p_heatmap <- plot_region_heatmap(x, chr, start, end, window_prop = window_prop, subsample = heatmap_subsample) +

             ggplot2::coord_cartesian(

                 xlim = xlim

             )

-

         p_out <- stack_plots(p_out, ggrastr::rasterise(p_heatmap, dpi = 300))

     }

@@ -85,6 +85,7 @@ setMethod("plot_region",

     }

 )

+#' @rdname plot_region

 #' @export

 setMethod("plot_region",

     signature(

@@ -135,6 +136,7 @@ setMethod("plot_region",

     }

 )

+#' @rdname plot_region

 #' @export

 setMethod("plot_region",

     signature(

@@ -186,6 +188,7 @@ setMethod("plot_region",

     }

 )

+#' @rdname plot_region

 #' @export

 setMethod("plot_region",

     signature(

@@ -20,6 +20,7 @@

 #' @param line_size the size of the lines.

 #' @param mod_scale the scale range for modification probabilities. Default c(0, 1), set to "auto" for automatic

 #'   limits.

+#' @param span DEPRECATED, use smoothing_window instead. Will be removed in next version.

 #'

 #' @details

 #' This function plots the methylation data for a given region. The region is specified by

@@ -56,7 +57,8 @@ setMethod("plot_region",

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

-        mod_scale = c(0, 1)

+        mod_scale = c(0, 1),

+        span = NULL

     ) {

         if (!missing("span")) {

             warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

@@ -105,7 +107,8 @@ setMethod("plot_region",

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

-        mod_scale = c(0, 1)

+        mod_scale = c(0, 1),

+        span = NULL

     ) {

         if (!missing("span")) {

             warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

@@ -155,7 +158,8 @@ setMethod("plot_region",

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

-        mod_scale = c(0, 1)

+        mod_scale = c(0, 1),

+        span = NULL

     ) {

         if (!missing("span")) {

             warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

@@ -205,7 +209,8 @@ setMethod("plot_region",

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

-        mod_scale = c(0, 1)

+        mod_scale = c(0, 1),

+        span = NULL

     ) {

         if (!missing("span")) {

             warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

@@ -12,7 +12,7 @@

 #' @param spaghetti whether or not individual reads should be shown.

 #' @param heatmap whether or not read-methylation heatmap should be shown.

 #' @param heatmap_subsample how many packed rows of reads to subsample to.

-#' @param span the span for loess smoothing.

+#' @param smoothing_window the window size for smoothing the trend line.

 #' @param window_prop the size of flanking region to plot. Can be a vector of two

 #'   values for left and right window size. Values indicate proportion of gene

 #'   length.

@@ -21,6 +21,15 @@

 #' @param mod_scale the scale range for modification probabilities. Default c(0, 1), set to "auto" for automatic

 #'   limits.

 #'

+#' @details

+#' This function plots the methylation data for a given region. The region is specified by

+#' chromosome, start and end positions. The basic plot contains a smoothed line plot of

+#' the methylation of each experimental group. Since V3.0.0 NanoMethViz has changed the

+#' smoothing strategy from a loess smoothing to a weighted moving average. This is because

+#' the loess smoothing was too computationally expensive for large datasets and had a

+#' span parameter that was difficult to tune. The new smoothing strategy is controlled

+#' by the smoothing_window argument.

+#'

 #' @examples

 #' nmr <- load_example_nanomethresult()

 #' plot_region(nmr, "chr7", 6703892, 6730431)

@@ -43,12 +52,15 @@ setMethod("plot_region",

         spaghetti = FALSE,

         heatmap = FALSE,

         heatmap_subsample = 50,

-        span = NULL,

+        smoothing_window = 500,

         window_prop = 0,

         palette = ggplot2::scale_colour_brewer(palette = "Set1"),

         line_size = 1,

         mod_scale = c(0, 1)

     ) {

+        if (!missing("span")) {

+            warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

+        }

         avg_method <- match.arg(avg_method)

         plot_region_impl(

@@ -71,8 +83,6 @@ setMethod("plot_region",

     }

 )

-#' @rdname plot_region

-#'

 #' @export

 setMethod("plot_region",

     signature(

@@ -97,6 +107,9 @@ setMethod("plot_region",

         line_size = 1,

         mod_scale = c(0, 1)

     ) {

+        if (!missing("span")) {

+            warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

+        }

         avg_method <- match.arg(avg_method)

         plot_region_impl(

@@ -119,8 +132,6 @@ setMethod("plot_region",

     }

 )

-#' @rdname plot_region

-#'

 #' @export

 setMethod("plot_region",

     signature(

@@ -146,6 +157,9 @@ setMethod("plot_region",

         line_size = 1,

         mod_scale = c(0, 1)

     ) {

+        if (!missing("span")) {

+            warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

+        }

         chr <- as.character(chr)

         avg_method <- match.arg(avg_method)

         plot_region(

@@ -159,7 +173,7 @@ setMethod("plot_region",

             spaghetti = spaghetti,

             heatmap = heatmap,

             heatmap_subsample = heatmap_subsample,

-            span = span,

+            smoothing_window = smoothing_window,

             window_prop = window_prop,

             palette = palette,

             line_size = line_size,

@@ -168,8 +182,6 @@ setMethod("plot_region",

     }

 )

-#' @rdname plot_region

-#'

 #' @export

 setMethod("plot_region",

     signature(

@@ -195,6 +207,9 @@ setMethod("plot_region",

         line_size = 1,

         mod_scale = c(0, 1)

     ) {

+        if (!missing("span")) {

+            warning("the 'span' argument has been deprecated, please use 'smoothing_window' instead")

+        }

         chr <- as.character(chr)

         avg_method <- match.arg(avg_method)

         plot_region(

@@ -208,7 +223,7 @@ setMethod("plot_region",

             spaghetti = spaghetti,

             heatmap = heatmap,

             heatmap_subsample = heatmap_subsample,

-            span = span,

+            smoothing_window = smoothing_window,

             window_prop = window_prop,

             palette = palette,

             line_size = line_size,

@@ -51,7 +51,7 @@ setMethod("plot_region",

     ) {

         avg_method <- match.arg(avg_method)

-        .plot_region(

+        plot_region_impl(

             x = x,

             chr = chr,

             start = start,

@@ -61,8 +61,8 @@ setMethod("plot_region",

             spaghetti = spaghetti,

             avg_method = avg_method,