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#' Plot gene aggregate plot
#'
#' @param genes a character vector of genes to include in aggregate plot, if NULL then all genes are used.
#' @inheritParams plot_agg_regions
#'
#' @return a ggplot object containing the aggregate methylation trend of genes.
#'
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#' @export
#'
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#' @examples
#' nmr <- load_example_nanomethresult()
#' plot_agg_genes(nmr)
#'
plot_agg_genes <- function(
x,
genes = NULL,
binary_threshold = 0.5,
group_col = NULL,
flank = 2000,
stranded = TRUE,
span = 0.05,
palette = ggplot2::scale_colour_brewer(palette = "Set1")
) {
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assertthat::assert_that(nrow(exons(x)) > 0, msg = "no exon annotations found in object")
gene_regions <- exons_to_genes(x)
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if (!is.null(genes)) {
gene_regions <- gene_regions %>%
filter(.data$symbol %in% genes)
}
plot_agg_regions(
x,
regions = gene_regions,
binary_threshold = binary_threshold,
group_col = group_col,
flank = flank,
stranded = stranded,
span = span,
palette = palette
)
}
plot_agg_tss <- function(
x,
genes = NULL,
binary_threshold = 0.5,
group_col = NULL,
flank = 2000,
stranded = TRUE,
span = 0.05,
palette = ggplot2::scale_colour_brewer(palette = "Set1")
) {
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assertthat::assert_that(nrow(exons(x)) > 0, msg = "no exon annotations found in object")
gene_regions <- exons_to_genes(x)
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if (!is.null(genes)) {
gene_regions <- gene_regions %>%
filter(.data$symbol %in% genes)
}
tss_regions <- gene_regions %>%
mutate(
start = case_when(
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strand == "+" ~ .data$start,
strand == "-" ~ .data$end,
TRUE ~ .data$start)
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) %>%
mutate(
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start = .data$start - flank,
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end = .data$start + 2 * flank
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)
kb_marker <- round(flank / 1000, 1)
labels <- c(
glue::glue("-{kb_marker}kb"),
"TSS",
glue::glue("+{kb_marker}kb")
)
p <- plot_agg_regions(
x,
regions = tss_regions,
binary_threshold = binary_threshold,
group_col = group_col,
flank = 0,
stranded = stranded,
span = span,
palette = palette
)
# hack to delete existing to avoid warning
p$scales$scales[[which(p$scales$find("x"))]] <- NULL
p + ggplot2::scale_x_continuous(
name = glue::glue(""),
breaks = c(0, 0.5, 1),
limits = c(0, 1),
labels = labels
)
}
plot_agg_tes <- function(
x,
genes = NULL,
binary_threshold = 0.5,
group_col = NULL,
flank = 2000,
stranded = TRUE,
span = 0.05,
palette = ggplot2::scale_colour_brewer(palette = "Set1")
) {
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assertthat::assert_that(nrow(exons(x)) > 0, msg = "no exon annotations found in object")
gene_regions <- exons_to_genes(x)
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if (!is.null(genes)) {
gene_regions <- gene_regions %>%
filter(.data$symbol %in% genes)
}
tes_regions <- gene_regions %>%
mutate(
start = case_when(
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strand == "+" ~ .data$end,
strand == "-" ~ .data$start,
TRUE ~ .data$end)
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) %>%
mutate(
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start = .data$start - flank,
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end = .data$start + 2 * flank
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)
kb_marker <- round(flank / 1000, 1)
labels <- c(
glue::glue("-{kb_marker}kb"),
"TES",
glue::glue("+{kb_marker}kb")
)
p <- plot_agg_regions(
x,
regions = tes_regions,
binary_threshold = binary_threshold,
group_col = group_col,
flank = 0,
stranded = stranded,
span = span,
palette = palette
)
# hack to delete existing to avoid warning
p$scales$scales[[which(p$scales$find("x"))]] <- NULL
p + ggplot2::scale_x_continuous(
name = glue::glue(""),
breaks = c(0, 0.5, 1),
limits = c(0, 1),
labels = labels
)
}
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