1. NanoMethViz
  2. R
  3. plot_agg_genes.R
Browse code

Added check for presence of exon annotation

shians authored on 27/05/2024 07:45:34
Showing 1 changed files
R/plot_agg_genes.R
History View file @ f8d9ab8
... ... 
@@ -21,7 +21,9 @@ plot_agg_genes <- function(
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     span = 0.05,
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     palette = ggplot2::scale_colour_brewer(palette = "Set1")
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 ) {
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-    gene_regions <- exons_to_genes(exons(x))
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+    assertthat::assert_that(nrow(exons(x)) > 0, msg = "no exon annotations found in object")
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+
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+    gene_regions <- exons_to_genes(x)
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     if (!is.null(genes)) {
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         gene_regions <- gene_regions %>%
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             filter(.data$symbol %in% genes)
... ... 
@@ -49,7 +51,9 @@ plot_agg_tss <- function(
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     span = 0.05,
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     palette = ggplot2::scale_colour_brewer(palette = "Set1")
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 ) {
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-    gene_regions <- exons_to_genes(exons(x))
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+    assertthat::assert_that(nrow(exons(x)) > 0, msg = "no exon annotations found in object")
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+
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+    gene_regions <- exons_to_genes(x)
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     if (!is.null(genes)) {
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         gene_regions <- gene_regions %>%
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             filter(.data$symbol %in% genes)
... ... 
@@ -103,7 +107,9 @@ plot_agg_tes <- function(
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     span = 0.05,
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     palette = ggplot2::scale_colour_brewer(palette = "Set1")
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 ) {
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-    gene_regions <- exons_to_genes(exons(x))
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+    assertthat::assert_that(nrow(exons(x)) > 0, msg = "no exon annotations found in object")
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+
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+    gene_regions <- exons_to_genes(x)
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     if (!is.null(genes)) {
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         gene_regions <- gene_regions %>%
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             filter(.data$symbol %in% genes)
Browse code

Linting

shians authored on 29/02/2024 05:18:23
Showing 1 changed files
R/plot_agg_genes.R
History View file @ 19dc3f0
... ... 
@@ -63,7 +63,7 @@ plot_agg_tss <- function(
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         ) %>%
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         mutate(
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             start = .data$start - flank,
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-            end = .data$start + 2*flank
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+            end = .data$start + 2 * flank
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         )
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     kb_marker <- round(flank / 1000, 1)
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     labels <- c(
... ... 
@@ -117,7 +117,7 @@ plot_agg_tes <- function(
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         ) %>%
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         mutate(
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             start = .data$start - flank,
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-            end = .data$start + 2*flank
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+            end = .data$start + 2 * flank
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         )
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     kb_marker <- round(flank / 1000, 1)
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     labels <- c(
Browse code

Exported `plot_agg_genes()`

Shians authored on 10/10/2022 06:34:21
Showing 1 changed files
R/plot_agg_genes.R
History View file @ 31c2e65
... ... 
@@ -5,6 +5,8 @@
5 5 
 #'
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 #' @return a ggplot object containing the aggregate methylation trend of genes.
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 #'
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+#' @export
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+#'
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 #' @examples
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 #' nmr <- load_example_nanomethresult()
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 #' plot_agg_genes(nmr)
... ... 
@@ -55,13 +57,13 @@ plot_agg_tss <- function(
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     tss_regions <- gene_regions %>%
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         mutate(
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             start = case_when(
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-                strand == "+" ~ start,
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-                strand == "-" ~ end,
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-                TRUE ~ start)
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+                strand == "+" ~ .data$start,
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+                strand == "-" ~ .data$end,
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+                TRUE ~ .data$start)
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         ) %>%
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         mutate(
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-            start = start - flank,
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-            end = start + 2*flank
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+            start = .data$start - flank,
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+            end = .data$start + 2*flank
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         )
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     kb_marker <- round(flank / 1000, 1)
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     labels <- c(
... ... 
@@ -109,13 +111,13 @@ plot_agg_tes <- function(
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     tes_regions <- gene_regions %>%
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         mutate(
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             start = case_when(
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-                strand == "+" ~ end,
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-                strand == "-" ~ start,
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-                TRUE ~ end)
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+                strand == "+" ~ .data$end,
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+                strand == "-" ~ .data$start,
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+                TRUE ~ .data$end)
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         ) %>%
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         mutate(
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-            start = start - flank,
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-            end = start + 2*flank
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+            start = .data$start - flank,
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+            end = .data$start + 2*flank
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         )
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     kb_marker <- round(flank / 1000, 1)
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     labels <- c(
Browse code

Fixed TES location when strand is *

Shians authored on 26/09/2022 01:46:55
Showing 1 changed files
R/plot_agg_genes.R
History View file @ 2d42a36
... ... 
@@ -111,7 +111,7 @@ plot_agg_tes <- function(
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             start = case_when(
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                 strand == "+" ~ end,
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                 strand == "-" ~ start,
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-                TRUE ~ start)
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+                TRUE ~ end)
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         ) %>%
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         mutate(
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             start = start - flank,
Browse code

Added utility aggregate plots `plot_agg_genes()`, `plot_agg_tss()` and `plot_agg_tes()`.

Shians authored on 08/09/2022 03:44:21
Showing 1 changed files
R/plot_agg_genes.R
History View file @ bb63e8d
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,146 @@
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+#' Plot gene aggregate plot
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+#'
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+#' @param genes a character vector of genes to include in aggregate plot, if NULL then all genes are used.
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+#' @inheritParams plot_agg_regions
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+#'
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+#' @return a ggplot object containing the aggregate methylation trend of genes.
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+#'
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+#' @examples
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+#' nmr <- load_example_nanomethresult()
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+#' plot_agg_genes(nmr)
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+#'
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+plot_agg_genes <- function(
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+    x,
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+    genes = NULL,
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+    binary_threshold = 0.5,
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+    group_col = NULL,
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+    flank = 2000,
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+    stranded = TRUE,
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+    span = 0.05,
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+    palette = ggplot2::scale_colour_brewer(palette = "Set1")
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+) {
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+    gene_regions <- exons_to_genes(exons(x))
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+    if (!is.null(genes)) {
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+        gene_regions <- gene_regions %>%
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+            filter(.data$symbol %in% genes)
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+    }
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+
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+    plot_agg_regions(
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+        x,
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+        regions = gene_regions,
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+        binary_threshold = binary_threshold,
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+        group_col = group_col,
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+        flank = flank,
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+        stranded = stranded,
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+        span = span,
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+        palette = palette
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+    )
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+}
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+
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+plot_agg_tss <- function(
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+    x,
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+    genes = NULL,
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+    binary_threshold = 0.5,
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+    group_col = NULL,
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+    flank = 2000,
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+    stranded = TRUE,
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+    span = 0.05,
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+    palette = ggplot2::scale_colour_brewer(palette = "Set1")
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+) {
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+    gene_regions <- exons_to_genes(exons(x))
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+    if (!is.null(genes)) {
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+        gene_regions <- gene_regions %>%
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+            filter(.data$symbol %in% genes)
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+    }
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+    tss_regions <- gene_regions %>%
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+        mutate(
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+            start = case_when(
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+                strand == "+" ~ start,
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+                strand == "-" ~ end,
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+                TRUE ~ start)
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+        ) %>%
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+        mutate(
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+            start = start - flank,
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+            end = start + 2*flank
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+        )
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+    kb_marker <- round(flank / 1000, 1)
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+    labels <- c(
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+        glue::glue("-{kb_marker}kb"),
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+        "TSS",
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+        glue::glue("+{kb_marker}kb")
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+    )
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+
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+    p <- plot_agg_regions(
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+        x,
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+        regions = tss_regions,
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+        binary_threshold = binary_threshold,
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+        group_col = group_col,
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+        flank = 0,
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+        stranded = stranded,
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+        span = span,
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+        palette = palette
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+    )
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+    # hack to delete existing to avoid warning
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+    p$scales$scales[[which(p$scales$find("x"))]] <- NULL
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+
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+    p + ggplot2::scale_x_continuous(
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+        name = glue::glue(""),
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+        breaks = c(0, 0.5, 1),
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+        limits = c(0, 1),
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+        labels = labels
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+    )
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+}
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+
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+plot_agg_tes <- function(
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+    x,
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+    genes = NULL,
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+    binary_threshold = 0.5,
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+    group_col = NULL,
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+    flank = 2000,
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+    stranded = TRUE,
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+    span = 0.05,
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+    palette = ggplot2::scale_colour_brewer(palette = "Set1")
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+) {
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+    gene_regions <- exons_to_genes(exons(x))
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+    if (!is.null(genes)) {
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+        gene_regions <- gene_regions %>%
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+            filter(.data$symbol %in% genes)
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+    }
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+    tes_regions <- gene_regions %>%
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+        mutate(
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+            start = case_when(
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+                strand == "+" ~ end,
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+                strand == "-" ~ start,
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+                TRUE ~ start)
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+        ) %>%
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+        mutate(
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+            start = start - flank,
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+            end = start + 2*flank
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+        )
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+    kb_marker <- round(flank / 1000, 1)
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+    labels <- c(
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+        glue::glue("-{kb_marker}kb"),
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+        "TES",
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+        glue::glue("+{kb_marker}kb")
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+    )
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+
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+    p <- plot_agg_regions(
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+        x,
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+        regions = tes_regions,
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+        binary_threshold = binary_threshold,
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+        group_col = group_col,
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+        flank = 0,
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+        stranded = stranded,
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+        span = span,
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+        palette = palette
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+    )
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+    # hack to delete existing to avoid warning
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+    p$scales$scales[[which(p$scales$find("x"))]] <- NULL
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+
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+    p + ggplot2::scale_x_continuous(
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+        name = glue::glue(""),
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+        breaks = c(0, 0.5, 1),
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+        limits = c(0, 1),
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+        labels = labels
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+    )
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+}