1. NanoMethViz
  2. Commit c5e99e0897057072ff265769c7b543cc576c10b8
Browse code

Added handling for exon annotations outside plot bounds

shians authored on 17/04/2020 06:39:11
Showing 2 changed files
R/plot_gene_annotation.R
History View file @ c5e99e0
... ... 
@@ -43,14 +43,18 @@ plot_gene_annotation <- function(exons_df, plot_start, plot_end) {
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             )
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         }
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-        out
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+        dplyr::rename(
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+            out,
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+            start = "gap_start",
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+            end = "gap_end"
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+        )
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     }
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     gap_pos <- .get_gaps(gap, "+")
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     gap_neg <- .get_gaps(gap, "-")
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     gap_none <- .get_gaps(gap, "*")
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-    gene_middle <- exons_df %>%
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+    gene_labels <- exons_df %>%
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         dplyr::group_by(.data$gene_id, .data$symbol, .data$transcript_id, .data$y_offset, .data$strand) %>%
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         dplyr::summarise(gene_middle = (min(.data$start) + max(.data$end)) / 2)
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... ... 
@@ -70,8 +74,8 @@ plot_gene_annotation <- function(exons_df, plot_start, plot_end) {
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     .connector_arrows <- function(gaps) {
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         ggplot2::geom_segment(
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             ggplot2::aes(
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-                x = .data$gap_start,
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-                xend = .data$gap_end,
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+                x = .data$start,
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+                xend = .data$end,
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                 y = .data$y_offset + 0.275,
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                 yend = .data$y_offset + 0.275
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             ),
... ... 
@@ -86,8 +90,8 @@ plot_gene_annotation <- function(exons_df, plot_start, plot_end) {
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     .connector_lines <- function(gaps) {
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         ggplot2::geom_segment(
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             ggplot2::aes(
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-                x = .data$gap_end,
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-                xend = .data$gap_start,
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+                x = .data$end,
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+                xend = .data$start,
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                 y = .data$y_offset + 0.275,
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                 yend = .data$y_offset + 0.275
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             ),
... ... 
@@ -95,32 +99,57 @@ plot_gene_annotation <- function(exons_df, plot_start, plot_end) {
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         )
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     }
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-    .gene_labels <- function(gene_middle) {
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-        gene_middle$symbol[gene_middle$strand == "+"] <- paste(
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-            gene_middle$symbol[gene_middle$strand == "+"],
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+    .gene_labels <- function(gene_labels) {
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+        gene_labels$symbol[gene_labels$strand == "+"] <- paste(
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+            gene_labels$symbol[gene_labels$strand == "+"],
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             ">"
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         )
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-        gene_middle$symbol[gene_middle$strand == "-"] <- paste(
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+        gene_labels$symbol[gene_labels$strand == "-"] <- paste(
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             "<",
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-            gene_middle$symbol[gene_middle$strand == "-"]
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+            gene_labels$symbol[gene_labels$strand == "-"]
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         )
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         ggplot2::geom_text(
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             aes(x = .data$gene_middle, y = .data$y_offset + 0.8, label = .data$symbol),
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-            data = gene_middle,
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+            data = gene_labels,
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             hjust = "center",
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             size = ggplot2::rel(3.5)
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         )
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     }
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+    .truncate_region <- function(x, plot_start, plot_end, strand) {
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+        if (strand == "-") {
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+            x <- x %>%
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+                dplyr::filter(end <= plot_end, start >= plot_start)
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+            x$end[x$end < plot_start] <- plot_start
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+            x$start[x$start > plot_end] <- plot_end
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+        } else {
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+            x <- x %>%
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+                dplyr::filter(start <= plot_end, end >= plot_start)
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+            x$start[x$start < plot_start] <- plot_start
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+            x$end[x$end > plot_end] <- plot_end
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+        }
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+
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+        x
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+    }
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+
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+    exons_df <- .truncate_region(exons_df, plot_start, plot_end, "*")
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+    gap_pos <- .truncate_region(gap_pos, plot_start, plot_end, "+")
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+    gap_neg <- .truncate_region(gap_neg, plot_start, plot_end, "-")
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+    gap_none <- .truncate_region(gap_none, plot_start, plot_end, "*")
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+    gene_labels <- gene_labels %>%
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+        dplyr::filter(
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+            dplyr::between(.data$gene_middle, plot_start, plot_end)
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+        )
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+
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     ggplot2::ggplot() +
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         ggplot2::theme_void() +
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         .exons(exons_df) +
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         .connector_arrows(gap_pos) +
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         .connector_arrows(gap_neg) +
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         .connector_lines(gap_none) +
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-        .gene_labels(gene_middle) +
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+        .gene_labels(gene_labels) +
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         ggplot2::xlim(plot_start, plot_end) +
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         ggplot2::ylim(0, 1 + max(exons_df$y_offset))
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 }
R/plot_methylation.R
History View file @ c5e99e0
... ... 
@@ -48,6 +48,7 @@ plot_methylation_internal <- function(
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                 aes(y = .data$mod_prop),
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                 geom = "smooth",
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                 method = "loess",
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+                na.rm = TRUE,
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                 size = 3,
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                 span = smooth_span,
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                 formula = y ~ x
... ... 
@@ -58,6 +59,7 @@ plot_methylation_internal <- function(
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                 aes(y = .data$mod_prob),
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                 geom = "smooth",
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                 method = "loess",
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+                na.rm = TRUE,
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                 size = 3,
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                 span = smooth_span,
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                 formula = y ~ x
... ... 
@@ -71,6 +73,7 @@ plot_methylation_internal <- function(
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                 alpha = 0.25,
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                 geom = "line",
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                 method = "loess",
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+                na.rm = TRUE,
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                 se = FALSE,
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                 span = 1,
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                 formula = y ~ x