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plot_gene_annotation <- function(exons_df, plot_start, plot_end) {
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| c1b1c7b3 |
# helper functions ----
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.exons <- function(exons_df) {
ggplot2::geom_rect(
ggplot2::aes(
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xmin = .data$start,
xmax = .data$end,
ymin = .data$y_offset + 0.05,
ymax = .data$y_offset + 0.55
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),
data = exons_df,
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fill = "#696969",
colour = "black"
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)
}
.connector_arrows <- function(gaps) {
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list(
# first half with arrow
ggplot2::geom_segment(
ggplot2::aes(
x = .data$start,
xend = (.data$start + .data$end)/2,
y = .data$y_offset + 0.275,
yend = .data$y_offset + 0.275
),
lineend = "butt",
linejoin = "mitre",
data = gaps,
arrow = grid::arrow(
type = "open",
length = ggplot2::unit(5, "points")
)
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),
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# second half without arrow
ggplot2::geom_segment(
ggplot2::aes(
x = (.data$start + .data$end)/2,
xend = .data$end,
y = .data$y_offset + 0.275,
yend = .data$y_offset + 0.275
),
lineend = "butt",
linejoin = "mitre",
data = gaps
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)
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)
}
.connector_lines <- function(gaps) {
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ggplot2::geom_segment(
ggplot2::aes(
|
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x = .data$end,
xend = .data$start,
|
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y = .data$y_offset + 0.275,
yend = .data$y_offset + 0.275
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),
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data = gaps
)
}
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.gene_labels <- function(gene_labels) {
gene_labels$symbol[gene_labels$strand == "+"] <- paste(
gene_labels$symbol[gene_labels$strand == "+"],
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">"
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)
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gene_labels$symbol[gene_labels$strand == "-"] <- paste(
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"<",
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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$label_pos, y = .data$y_offset + 0.8, label = .data$symbol),
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data = gene_labels,
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hjust = "center",
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size = ggplot2::rel(2.5)
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)
}
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.filter_regions <- function(exons_df, plot_start, plot_end) {
transcripts <- exons_df %>%
dplyr::summarise(
|
| f3668239 |
.by = "transcript_id",
|
| c1b1c7b3 |
start = min(.data$start),
end = max(.data$end)
)
transcripts <- transcripts %>%
dplyr::filter(
.data$start <= plot_end & .data$end >= plot_start
)
exons_df %>%
dplyr::filter(
.data$transcript_id %in% transcripts$transcript_id
)
}
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.truncate_region <- function(x, plot_start, plot_end, strand) {
if (strand == "-") {
x <- x %>%
|
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dplyr::filter(.data$end <= plot_end, .data$start >= plot_start)
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x$end[x$end < plot_start] <- plot_start
x$start[x$start > plot_end] <- plot_end
} else {
x <- x %>%
|
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dplyr::filter(.data$start <= plot_end, .data$end >= plot_start)
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x$start[x$start < plot_start] <- plot_start
x$end[x$end > plot_end] <- plot_end
}
x
}
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.get_gaps <- function(gaps, strand = c("+", "-", "*")) {
strand <- match.arg(strand)
gaps <- gaps %>%
split(gaps$strand)
if (!is.null(gaps[[strand]])) {
out <- gaps[[strand]]
if (strand == "-") {
temp <- out$gap_start
out$gap_start <- out$gap_end
out$gap_end <- temp
}
} else {
out <- tibble::tibble(
uid = character(0),
y_offset = numeric(0),
strand = character(0),
gap_start = integer(0),
gap_end = integer(0)
)
}
dplyr::rename(
out,
start = "gap_start",
end = "gap_end"
)
}
# function body ----
if (nrow(exons_df) == 0) {
p <- ggplot() + theme_void()
attr(p, "plot_height") <- 0
return(p)
}
# remove transcripts outside plot area
exons_df <- .filter_regions(exons_df, plot_start, plot_end)
exons_df <- exons_df %>%
dplyr::mutate(
uid = factor(paste(.data$gene_id, .data$transcript_id, sep = ".")),
y_offset = as.integer(.data$uid) - 1
)
exons_count <- exons_df %>%
dplyr::group_by(.data$uid) %>%
dplyr::summarise(exons = dplyr::n())
gap <- exons_df %>%
dplyr::inner_join(exons_count, by = c("uid"), multiple = "all") %>%
dplyr::filter(.data$exons > 1) %>%
dplyr::group_by("transcript_id") %>%
dplyr::arrange(.data$start) %>%
dplyr::ungroup()
if (nrow(gap) > 0) {
gap <- gap %>%
dplyr::group_by(.data$uid, .data$strand, .data$y_offset) %>%
dplyr::summarise(
gap_start = list(.data$end[-length(.data$end)]),
gap_end = list(.data$start[-1])
) %>%
tidyr::unnest(cols = c("gap_start", "gap_end"))
} else {
gap <- tibble::tibble(
uid = character(),
y_offset = numeric(),
strand = character(),
gap_start = numeric(),
gap_end = numeric()
)
}
gap_pos <- .get_gaps(gap, "+")
gap_neg <- .get_gaps(gap, "-")
gap_none <- .get_gaps(gap, "*")
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region_width <- plot_end - plot_start
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gene_labels <- exons_df %>%
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$end)) / 2,
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label_pos = .data$gene_middle,
label_pos = pmin(.data$label_pos, plot_end - region_width * 0.05),
label_pos = pmax(.data$label_pos, plot_start + region_width * 0.05)
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)
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| c1b1c7b3 |
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exons_df <- .truncate_region(exons_df, plot_start, plot_end, "*")
|
| c1b1c7b3 |
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gap_pos <- .truncate_region(gap_pos, plot_start, plot_end, "+")
gap_neg <- .truncate_region(gap_neg, plot_start, plot_end, "-")
gap_none <- .truncate_region(gap_none, plot_start, plot_end, "*")
gene_labels <- gene_labels %>%
dplyr::filter(
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dplyr::between(.data$label_pos, plot_start, plot_end)
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)
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if (length(exons_df$y_offset) > 0) {
plot_height <- 1 + max(exons_df$y_offset)
} else {
plot_height <- 0
}
p <- ggplot2::ggplot() +
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| 7aa2a454 |
ggplot2::theme_void() +
.connector_arrows(gap_pos) +
.connector_arrows(gap_neg) +
.connector_lines(gap_none) +
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.exons(exons_df) +
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.gene_labels(gene_labels) +
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ggplot2::ylim(0, plot_height)
attr(p, "plot_height") <- plot_height
p
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}
|
