R/plotSelf.R
In daewoooo/SVbyEye: Visualization of genomic structural variants
Defines functions
plotSelf
Documented in
plotSelf
#' Make a horizontal sequence self-alignments.
#'
#' This function takes self-alignment coordinates generated by 'minimap2' aligner and
#' visualize them either as horizontal 'dotplot' or arcs.
#'
#' @param shape A shape used to plot aligned sequences: Either 'segment', 'arc' or 'arrow'.
#' @param sort.by Order PAF alignments by relative left-most coordinates ('position') or by the alignment length ('length').
#' @param highlight.pos A single or a set of positions to be highlighted as vertical solid lines.
#' @param highlight.region A pair of positions to be highlighted as vertical range.
#' @inheritParams breakPaf
#' @inheritParams pafAlignmentToBins
#' @inheritParams plotMiro
#' @return A \code{ggplot2} object.
#' @import ggplot2
#' @importFrom grid unit
#' @importFrom scales comma
#' @importFrom wesanderson wes_palette
#' @importFrom dplyr group_by mutate arrange bind_rows desc
#' @author David Porubsky
#' @export
#' @examples
#' ## Get PAF to plot
#' paf.file <- system.file("extdata", "test2.paf", package = "SVbyEye")
#' ## Read in PAF
#' paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
#' ## Make a plot
#' ## Plot alignment as horizontal dotplots and color by alignment directionality
#' plotSelf(paf.table = paf.table, color.by = "direction", shape = "segment")
#' ## Plot alignment as arcs and color by alignment directionality
#' plotSelf(paf.table = paf.table, color.by = "direction", shape = "arc")
#' ## Plot alignment as arrows and color by alignment directionality
#' plotSelf(paf.table = paf.table, color.by = "direction", shape = "arrow")
#' ## Highlight structural variants within self-alignments
#' plotSelf(
#' paf.table = paf.table, min.deletion.size = 50, min.insertion.size = 50,
#' highlight.sv = "outline"
#' )
#' ## Highlight structural variants using arc shapes
#' plotSelf(
#' paf.table = paf.table, min.deletion.size = 50, min.insertion.size = 50,
#' highlight.sv = "outline", shape = "arc"
#' )
#' ## Highlight structural variants within arrow shapes
#' plotSelf(
#' paf.table = paf.table, min.deletion.size = 50, min.insertion.size = 50,
#' highlight.sv = "outline", shape = "arrow"
#' )
#' ## Bin PAF alignments into user defined bin and color them by sequence identity (% of matched bases)
#' plotSelf(paf.table = paf.table, binsize = 1000)
#' plotSelf(paf.table = paf.table, binsize = 1000, shape = "arc")
#' ## Add annotation to self-alignments ##
#' annot.file <- system.file("extdata", "test2.sd.annot.RData", package = "SVbyEye")
#' annot.gr <- get(load(annot.file))
#' plt <- plotSelf(paf.table = paf.table, color.by = "direction", shape = "arc")
#' ## Add annotation to a new level
#' addAnnotation(ggplot.obj = plt, annot.gr = annot.gr, coordinate.space = "self")
#' ## Add annotation to the alignment level
#' plt <- plotSelf(
#' paf.table = paf.table, color.by = "direction", shape = "arc",
#' add.alignment.arrows = FALSE
#' )
#' addAnnotation(
#' ggplot.obj = plt, annot.gr = annot.gr, coordinate.space = "self",
#' annotation.level = 0
#' )
#'
plotSelf <- function(paf.table = NULL, min.deletion.size = NULL, min.insertion.size = NULL, highlight.sv = NULL, binsize = NULL, shape = "segment", sort.by = "position", color.by = "direction", color.palette = NULL, add.alignment.arrows = TRUE, highlight.pos = NULL, highlight.region = NULL) {
## Check user input ##
## Make sure submitted paf.table has at least 12 mandatory fields
if (ncol(paf.table) >= 12) {
paf <- paf.table
## Add PAF alignment IDs if it doesn't exists
if (!"aln.id" %in% colnames(paf)) {
paf$aln.id <- seq_len(nrow(paf))
}
} else {
stop("Submitted PAF alignments do not contain a minimum of 12 mandatory fields, see PAF file format definition !!!")
}
## If desired visualization shape is 'arrow' binning is not allowed
if (shape == "arrow" & !is.null(binsize)) {
binsize <- NULL
message("[plotSelf] Binning is not available for shape = 'arrow', setting binsize = NULL.")
}
## Apply self-alignment specific set of filters ##
## Keep only self-alignments (query and target names have to be the same)
paf <- paf[paf$q.name == paf$t.name, ]
if (nrow(paf) == 0) {
stop("No self-alignments present in submitted 'paf.table', self-alignments are expected to have the same value in 'q.name' and 't.name' field !!!")
}
## Remove diagonals (self-alignments) with the same start and end position
paf <- paf[!(paf$q.start == paf$t.start & paf$q.end == paf$t.end), ]
## Due to the minimap2 self-alignment redundancy keep only alignments where query start is smaller than the target start
paf <- paf[paf$q.start < paf$t.start, ]
## Break PAF at insertion/deletions defined in cigar string
if (!is.null(min.deletion.size) | !is.null(min.insertion.size)) {
## Check user input
if (is.null(min.deletion.size)) {
min.deletion.size <- 0
}
if (is.null(min.insertion.size)) {
min.insertion.size <- 0
}
if (min.deletion.size > 0 | min.insertion.size > 0) {
paf.l <- breakPaf(paf.table = paf, min.deletion.size = min.deletion.size, min.insertion.size = min.insertion.size, collapse.mismatches = TRUE, report.sv = TRUE)
paf <- paf.l$M
paf.svs <- paf.l$SVs
}
} else {
paf.svs <- NULL
if (!is.null(highlight.sv)) {
highlight.sv <- NULL
warning("Please specify 'min.deletion.size' and 'min.insertion.size' in order to make parameter 'highlight.sv' to work !!!")
}
}
## Store PAF alignments for later addition of 'geom_gene_arrow'
paf.copy <- paf
paf.copy$ID <- "M"
## Bin PAF alignments
if (!is.null(binsize)) {
if (binsize > 0) {
if (binsize < 10) {
binsize <- 10
warning("Minimum allowed bin size is 10, forced binsize=10!!!")
}
paf <- pafToBins(paf.table = paf, binsize = binsize)
## If the PAF alignments are binned only color.by = 'fraction.matches' is allowed
color.by <- "identity"
}
}
## Mark alignments ranges by 'M' (matches)
paf$ID <- "M"
## Add SVs to the alignment table
if (!is.null(paf.svs)) {
if (nrow(paf.svs) > 0) {
paf.svs$ID <- "INS"
paf.svs$ID[grep(paf.svs$cg, pattern = "D", ignore.case = TRUE)] <- "DEL"
paf <- dplyr::bind_rows(paf, paf.svs)
}
}
## Prepare data for plotting ##
## When dealing with self-alignments query (left-most) sequence is denoted as s1 and target (right-most) sequence is s2
paf <- paf[paf$ID == "M", ]
coords <- data.frame(
s1.start = paf$q.start,
s1.end = paf$q.end,
s2.start = paf$t.start,
s2.end = paf$t.end,
s1.width = (paf$q.end - paf$q.start) + 1,
s2.width = (paf$t.end - paf$t.start) + 1,
seq.name = paste(unique(paf$q.name, paf$t.name), collapse = "_"),
seq.id = "self",
dir = paf$strand,
n.match = paf$n.match,
aln.len = paf$aln.len,
identity = (paf$n.match / paf$aln.len) * 100,
aln.id = paf$aln.id,
stringsAsFactors = FALSE
)
## Add color.by column if defined
if (color.by %in% colnames(paf)) {
coords[, color.by] <- paf[, color.by]
}
## Get max position (for x-axis plotting)
max.pos <- unique(paf$q.len)
## Flip start and end for reverse oriented alignments
coords[coords$dir == "-", ] <- transform(coords[coords$dir == "-", ],
"s2.start" = coords[coords$dir == "-", ]$s2.end,
"s2.end" = coords[coords$dir == "-", ]$s2.start
)
## Sort alignments
if (sort.by == "position") {
## Order alignments by query position
ord.aln.id <- coords %>%
dplyr::group_by(.data$aln.id) %>%
dplyr::summarise(start.id = min(.data$s1.start)) %>%
dplyr::arrange(.data$start.id)
coords$aln.id <- factor(coords$aln.id, levels = ord.aln.id$aln.id)
coords <- coords %>%
dplyr::group_by(.data$aln.id) %>%
dplyr::arrange(.data$s1.start, .by_group = TRUE)
} else if (sort.by == "length") {
## Order alignments by alignment length
coords <- coords %>%
dplyr::group_by(.data$aln.id) %>%
dplyr::mutate(length.id = sum(.data$aln.len)) %>%
dplyr::arrange(dplyr::desc(.data$length.id), .data$s1.start)
} else {
## Order by alignment id
coords <- coords %>% dplyr::arrange(.data$aln.id, .data$s1.start)
}
## Make self-dotplot ##
#######################
## Define color palette for alignment directionality
if (!is.null(color.palette)) {
if (all(c("+", "-") %in% names(color.palette))) {
pal <- color.palette
} else {
pal <- c("-" = "cornflowerblue", "+" = "forestgreen")
warning("User defined 'color.palette' does not contain both '+' and '-' directions, using default values instead!!!")
}
} else {
pal <- c("-" = "cornflowerblue", "+" = "forestgreen")
}
## Define discrete color palettes
if (color.by == "direction") {
coords$col.levels <- factor(coords$dir, levels = c("+", "-"))
} else if (color.by == "identity") {
coords$identity[is.nan(coords$identity) | is.na(coords$identity)] <- 0
## Define color scheme
coords.l <- getColorScheme(data.table = coords, value.field = "identity", breaks = c(90, 95, 99, 99.5, 99.6, 99.7, 99.8, 99.9))
coords <- coords.l$data
coords$identity <- coords$col.levels
colors <- coords.l$colors
} else if (color.by %in% colnames(paf)) {
## Define color scheme
coords.l <- getColorScheme(data.table = coords, value.field = color.by)
coords <- coords.l$data
colors <- coords.l$colors
} else {
color.by <- "direction"
}
## Define plotting coordinates
if (shape == "segment") {
coords$y1 <- 0
coords$y1end <- 0
coords$y2 <- 0
coords$y2end <- 0
for (i in seq_len(nrow(coords))) {
row.df <- coords[i, ]
if (i == 1) {
row.df$y1 <- 1
row.df$y2 <- 1
row.df$y1end <- row.df$s1.width
row.df$y2end <- row.df$s2.width
offset <- max(row.df$y1end, row.df$y2end)
} else {
row.df$y1 <- offset
row.df$y2 <- offset
row.df$y1end <- offset + row.df$s1.width
row.df$y2end <- offset + row.df$s2.width
offset <- max(row.df$y1end, row.df$y2end)
}
coords[i, ] <- row.df
}
## Get polygon coordinates
plt.dir.df <- coords[coords$dir == "+", ]
plt.rev.df <- coords[coords$dir == "-", ]
if (nrow(plt.dir.df) > 0) {
poly.dir.df <- data.frame(
x = c(rbind(plt.dir.df$s1.start, plt.dir.df$s2.start, plt.dir.df$s2.end, plt.dir.df$s1.end)),
# y=c(rbind(plt.dir.df$y1, plt.dir.df$y2, plt.dir.df$y1end, plt.dir.df$y2end)),
y = c(rbind(plt.dir.df$y1, plt.dir.df$y2, plt.dir.df$y2end, plt.dir.df$y1end)),
group = rep(seq_len(nrow(plt.dir.df)), each = 4),
seq.id = plt.dir.df$seq.id,
seq.name = plt.dir.df$seq.name,
col.levels = rep(plt.dir.df$col.levels, each = 4)
)
} else {
poly.dir.df <- data.frame(
x = c(rbind(NaN, NaN, NaN, NaN)),
y = c(rbind(NaN, NaN, NaN, NaN)),
group = rep(1, each = 4),
seq.id = NA,
seq.name = NA,
col.levels = factor(NA, levels(coords$col.levels))
)
}
if (nrow(plt.rev.df) > 0) {
poly.rev.df <- data.frame(
x = c(rbind(plt.rev.df$s1.start, plt.rev.df$s1.end, plt.rev.df$s2.end, plt.rev.df$s2.start)),
y = c(rbind(plt.rev.df$y1, plt.rev.df$y1end, plt.rev.df$y2end, plt.rev.df$y2)),
group = rep(seq_len(nrow(plt.rev.df)), each = 4),
seq.id = plt.rev.df$seq.id,
seq.name = plt.rev.df$seq.name,
col.levels = rep(plt.rev.df$col.levels, each = 4)
)
} else {
poly.rev.df <- data.frame(
x = c(rbind(NaN, NaN, NaN, NaN)),
y = c(rbind(NaN, NaN, NaN, NaN)),
group = rep(1, each = 4),
seq.id = NA,
seq.name = NA,
col.levels = factor(NA, levels(coords$col.levels))
)
}
## Make segment dotplot
y.limit <- max(c(coords$y1end, coords$y2end))
## Plot alignment pairs
plt <- ggplot2::ggplot(coords) +
ggplot2::geom_segment(ggplot2::aes(x = .data$s1.start, xend = .data$s1.end, y = .data$y1, yend = .data$y1end)) +
ggplot2::geom_segment(ggplot2::aes(x = .data$s2.start, xend = .data$s2.end, y = .data$y2, yend = .data$y2end)) +
ggplot2::geom_polygon(data = poly.dir.df, ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, fill = .data$col.levels), alpha = 0.5) +
ggplot2::geom_polygon(data = poly.rev.df, ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, fill = .data$col.levels), alpha = 0.5) +
ggplot2::scale_x_continuous(labels = scales::comma, expand = c(0, 0), limits = c(0, max.pos)) +
# ggplot2::scale_y_continuous(limits = c(-1, y.limit), expand = c(0.1, 0.1)) +
ggplot2::scale_y_continuous(expand = c(0.1, 0.1)) +
# ggplot2::coord_cartesian(xlim = c(0, max.pos)) +
ggplot2::ylab("Self-alignments") +
ggplot2::xlab("Contig position (bp)")
## Define alignment color scheme
if (color.by == "direction") {
plt <- plt + ggplot2::scale_fill_manual(values = pal, drop = FALSE, name = "Alignment\ndirection")
} else {
plt <- plt + ggplot2::scale_fill_manual(values = colors, drop = FALSE, name = eval(color.by))
}
# coord_fixed(ratio = 1) +
## Add indels
if (!is.null(highlight.sv)) {
if (nrow(paf.svs) > 0) {
## Define SV ranges
## Insertions belong to query coordinates and deletions to target coordinates
ins <- paf.svs[paf.svs$ID == "INS", c("q.name", "q.start", "q.end", "ID")]
colnames(ins) <- c("seqnames", "start", "end", "ID")
del <- paf.svs[paf.svs$ID == "DEL", c("t.name", "t.start", "t.end", "ID")]
colnames(del) <- c("seqnames", "start", "end", "ID")
coords.svs <- dplyr::bind_rows(ins, del)
## Add SVs to the plot
if (highlight.sv == "outline") {
plt <- plt + ggnewscale::new_scale_color() +
ggplot2::geom_rect(data = coords.svs, ggplot2::aes(xmin = .data$start, xmax = .data$end, ymin = -Inf, ymax = Inf, color = .data$ID), fill = NA, alpha = 0.5, inherit.aes = FALSE) +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else if (highlight.sv == "fill") {
plt <- plt + ggnewscale::new_scale_fill() + ggnewscale::new_scale_color() +
ggplot2::geom_rect(data = coords.svs, ggplot2::aes(xmin = .data$start, xmax = .data$end, ymin = -Inf, ymax = Inf, fill = .data$ID, color = .data$ID), size = 0.2, alpha = 0.5, inherit.aes = FALSE) +
ggplot2::scale_fill_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class") +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else {
warning("Parameter 'highlight.sv' can only take values 'outline' or 'fill', see function documentation!!!")
}
} else {
message("There are no SVs to highlight. Try to decrease 'min.deletion.size' and 'min.insertion.size' values!!!")
}
}
} else if (shape == "arc") {
## Get arc coordinates
x <- c(rbind(coords$s1.start, coords$s2.start, coords$s1.end, coords$s2.end))
group <- rep(seq_len(nrow(coords)), each = 4)
seq.id <- "self"
seq.name <- unique(coords$seq.name)
col.levels <- rep(coords$col.levels, each = 4)
plt.df <- data.frame(
x = x,
y = 0,
group = group,
seq.id = seq.id,
seq.name = seq.name,
col.levels = col.levels
)
plt <- ggplot2::ggplot(plt.df) +
geom_wide_arc(ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, fill = .data$col.levels), alpha = 0.5) +
ggplot2::scale_x_continuous(labels = scales::comma, expand = c(0, 0), limits = c(0, max.pos)) +
# ggplot2::coord_cartesian(xlim = c(0, max.pos)) +
ggplot2::ylab("Self-alignments") +
ggplot2::xlab("Contig position (bp)")
## Define alignment color scheme
if (color.by == "direction") {
plt <- plt + ggplot2::scale_fill_manual(values = pal, drop = FALSE, name = "Alignment\ndirection")
} else {
plt <- plt + ggplot2::scale_fill_manual(values = colors, drop = FALSE, name = eval(color.by))
}
## Add indels
if (!is.null(highlight.sv)) {
if (nrow(paf.svs) > 0) {
## Define SV ranges
x <- c(rbind(paf.svs$q.start, paf.svs$t.start, paf.svs$q.end, paf.svs$t.end))
group <- rep(seq_len(nrow(paf.svs)), each = 4)
# seq.id <- c(rbind("s1", "s2", "s1", "s2"))
direction <- rep(paf.svs$strand, each = 4)
ID <- rep(paf.svs$ID, each = 4)
svs.df <- data.frame(
x = x,
y = 0,
group = group,
# seq.id = seq.id,
# seq.name = seq.name,
direction = direction,
ID = ID
)
## Add SVs to the plot
if (highlight.sv == "outline") {
plt <- plt + ggnewscale::new_scale_color() +
geom_wide_arc(data = svs.df, ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, color = .data$ID), fill = NA, alpha = 0.5, inherit.aes = FALSE) +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else if (highlight.sv == "fill") {
plt <- plt + ggnewscale::new_scale_fill() + ggnewscale::new_scale_color() +
geom_wide_arc(data = svs.df, ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, fill = .data$ID, color = .data$ID), size = 0.2, alpha = 0.5, inherit.aes = FALSE) +
ggplot2::scale_fill_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class") +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else {
warning("Parameter 'highlight.sv' can only take values 'outline' or 'fill', see function documentation!!!")
}
} else {
message("There are no SVs to highlight. Try to decrease 'min.deletion.size' and 'min.insertion.size' values!!!")
}
}
} else if (shape == "arrow") {
## Do not add alignment arrows if main shape is arrow
add.alignment.arrows <- FALSE
## Make Arrow plot
arrow.df <- data.frame(
xmin = c(coords$s1.start, coords$s2.start),
xmax = c(coords$s1.end, coords$s2.end),
y = as.numeric(coords$aln.id),
col.levels = factor(c(rep("+", nrow(coords)), coords$dir), levels = c("+", "-")), # to make sure s1 is always forward
seq.id = "self",
seq.name = unique(coords$seq.name)
)
arrow.links <- data.frame(
xmin = pmax(coords$s1.start, coords$s1.end),
xmax = pmin(coords$s2.start, coords$s2.end),
y = as.numeric(coords$aln.id)
)
arrow.df$dir <- ifelse(arrow.df$col.levels == "+", 1, 0)
## Make sure start is always smaller than end of the alignment
arrow.df[, c("xmin", "xmax")] <- t(apply(arrow.df[, c("xmin", "xmax")], 1, sort))
## Plot arrows
plt <- ggplot2::ggplot() +
ggplot2::geom_segment(data = arrow.links, aes(x = .data$xmin, xend = .data$xmax, y = .data$y, yend = .data$y), linetype = "solid") +
gggenes::geom_gene_arrow(data = arrow.df, ggplot2::aes(xmin = .data$xmin, xmax = .data$xmax, y = .data$y, forward = .data$dir, fill = .data$col.levels), arrowhead_height = grid::unit(3, "mm")) +
ggplot2::scale_fill_manual(values = pal, name = "Alignment\ndirection") +
ggplot2::scale_x_continuous(labels = scales::comma, expand = c(0, 0), limits = c(0, max.pos)) +
# ggplot2::scale_y_continuous(expand = c(0.1, 0.1)) +
ggplot2::scale_y_continuous(expand = c(grid::unit(0.1, "mm"), grid::unit(0.1, "mm"))) +
# ggplot2::coord_cartesian(xlim = c(0, max.pos)) +
ggplot2::ylab("Self-alignments") +
ggplot2::xlab("Contig position (bp)")
## Add indels
if (!is.null(highlight.sv)) {
if (nrow(paf.svs) > 0) {
## Define SV ranges
## Insertions belong to query coordinates and deletions to target coordinates
ins <- paf.svs[paf.svs$ID == "INS", c("q.name", "q.start", "q.end", "aln.id", "ID")]
colnames(ins) <- c("seqnames", "start", "end", "aln.id", "ID")
del <- paf.svs[paf.svs$ID == "DEL", c("t.name", "t.start", "t.end", "aln.id", "ID")]
colnames(del) <- c("seqnames", "start", "end", "aln.id", "ID")
coords.svs <- dplyr::bind_rows(ins, del)
## Add SVs to the plot
if (highlight.sv == "outline") {
plt <- plt + ggnewscale::new_scale_color() +
geom_roundrect(data = coords.svs, ggplot2::aes(xmin = .data$start, xmax = .data$end, y = aln.id, color = .data$ID), fill = NA, inherit.aes = FALSE, radius = grid::unit(0, "mm")) +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else if (highlight.sv == "fill") {
plt <- plt + ggnewscale::new_scale_fill() + ggnewscale::new_scale_color() +
geom_roundrect(data = coords.svs, ggplot2::aes(xmin = .data$start, xmax = .data$end, y = aln.id, fill = .data$ID, color = .data$ID), size = 0.2, inherit.aes = FALSE, radius = grid::unit(0, "mm")) +
ggplot2::scale_fill_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class") +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else {
warning("Parameter 'highlight.sv' can only take values 'outline' or 'fill', see function documentation!!!")
}
} else {
message("There are no SVs to highlight. Try to decrease 'min.deletion.size' and 'min.insertion.size' values!!!")
}
}
} else {
warning("Paremeter shape can only take values 'segment', 'arc' or 'arrow' !!!")
plt <- ggplot() +
scale_fill_manual(values = pal) +
ylab("Self-alignments") +
xlab("Contig position (bp)") +
theme_minimal() +
theme(
axis.text.y = element_blank(),
axis.ticks.y = element_blank()
)
}
## Add alignment arrows ##
if (add.alignment.arrows) {
arrow.df <- data.frame(
"xmin" = c(rbind(paf.copy$q.start, paf.copy$t.start)),
"xmax" = c(rbind(paf.copy$q.end, paf.copy$t.end)),
"col.levels" = factor(c(rbind("+", paf.copy$strand)), levels = c("+", "-"))
) # to make sure s1 is always forward
arrow.df$dir <- ifelse(arrow.df$col.levels == "+", 1, 0)
## Make sure start is always smaller than end of the alignment
arrow.df[, c("xmin", "xmax")] <- t(apply(arrow.df[, c("xmin", "xmax")], 1, sort))
## Plot arrows
plt <- plt + ggnewscale::new_scale_fill() +
gggenes::geom_gene_arrow(data = arrow.df, ggplot2::aes(xmin = .data$xmin, xmax = .data$xmax, y = 0, forward = .data$dir, fill = .data$col.levels), arrowhead_height = grid::unit(3, "mm")) +
ggplot2::scale_fill_manual(values = pal, name = "Alignment\ndirection")
}
## Highlight user defined positions
if (!is.null(highlight.pos) & is.numeric(highlight.pos)) {
highlight.pos <- highlight.pos[highlight.pos > 0 & highlight.pos <= max.pos]
if (length(highlight.pos) > 0) {
plt <- plt + ggplot2::geom_vline(xintercept = highlight.pos)
}
}
## Highlight user defined region
if (!is.null(highlight.region)) {
highlight.region <- highlight.region[highlight.region$xmin > 0 & highlight.region$xmax <= max.pos, ]
if (nrow(highlight.region) > 0) {
plt <- plt + ggplot2::geom_rect(data = highlight.region, ggplot2::aes(xmin = .data$xmin, xmax = .data$xmax, ymin = 0, ymax = Inf), color = "red", alpha = 0.25)
}
}
## Set the theme
theme_self <- ggplot2::theme(
panel.grid.major = ggplot2::element_blank(),
panel.grid.minor = ggplot2::element_blank(),
panel.background = ggplot2::element_blank(),
axis.line.x = ggplot2::element_line(linewidth = 1),
axis.ticks.x = ggplot2::element_line(linewidth = 1),
axis.ticks.length.x = grid::unit(2, "mm"),
axis.text.y = ggplot2::element_blank(),
axis.ticks.y = ggplot2::element_blank()
)
plt <- plt + theme_self
## Return final plot
return(plt)
}
daewoooo/SVbyEye documentation built on Oct. 15, 2024, 6:12 a.m.
R Package Documentation
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Defines functions plotSelf
Documented in plotSelf
#' Make a horizontal sequence self-alignments.
#'
#' This function takes self-alignment coordinates generated by 'minimap2' aligner and
#' visualize them either as horizontal 'dotplot' or arcs.
#'
#' @param shape A shape used to plot aligned sequences: Either 'segment', 'arc' or 'arrow'.
#' @param sort.by Order PAF alignments by relative left-most coordinates ('position') or by the alignment length ('length').
#' @param highlight.pos A single or a set of positions to be highlighted as vertical solid lines.
#' @param highlight.region A pair of positions to be highlighted as vertical range.
#' @inheritParams breakPaf
#' @inheritParams pafAlignmentToBins
#' @inheritParams plotMiro
#' @return A \code{ggplot2} object.
#' @import ggplot2
#' @importFrom grid unit
#' @importFrom scales comma
#' @importFrom wesanderson wes_palette
#' @importFrom dplyr group_by mutate arrange bind_rows desc
#' @author David Porubsky
#' @export
#' @examples
#' ## Get PAF to plot
#' paf.file <- system.file("extdata", "test2.paf", package = "SVbyEye")
#' ## Read in PAF
#' paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
#' ## Make a plot
#' ## Plot alignment as horizontal dotplots and color by alignment directionality
#' plotSelf(paf.table = paf.table, color.by = "direction", shape = "segment")
#' ## Plot alignment as arcs and color by alignment directionality
#' plotSelf(paf.table = paf.table, color.by = "direction", shape = "arc")
#' ## Plot alignment as arrows and color by alignment directionality
#' plotSelf(paf.table = paf.table, color.by = "direction", shape = "arrow")
#' ## Highlight structural variants within self-alignments
#' plotSelf(
#' paf.table = paf.table, min.deletion.size = 50, min.insertion.size = 50,
#' highlight.sv = "outline"
#' )
#' ## Highlight structural variants using arc shapes
#' plotSelf(
#' paf.table = paf.table, min.deletion.size = 50, min.insertion.size = 50,
#' highlight.sv = "outline", shape = "arc"
#' )
#' ## Highlight structural variants within arrow shapes
#' plotSelf(
#' paf.table = paf.table, min.deletion.size = 50, min.insertion.size = 50,
#' highlight.sv = "outline", shape = "arrow"
#' )
#' ## Bin PAF alignments into user defined bin and color them by sequence identity (% of matched bases)
#' plotSelf(paf.table = paf.table, binsize = 1000)
#' plotSelf(paf.table = paf.table, binsize = 1000, shape = "arc")
#' ## Add annotation to self-alignments ##
#' annot.file <- system.file("extdata", "test2.sd.annot.RData", package = "SVbyEye")
#' annot.gr <- get(load(annot.file))
#' plt <- plotSelf(paf.table = paf.table, color.by = "direction", shape = "arc")
#' ## Add annotation to a new level
#' addAnnotation(ggplot.obj = plt, annot.gr = annot.gr, coordinate.space = "self")
#' ## Add annotation to the alignment level
#' plt <- plotSelf(
#' paf.table = paf.table, color.by = "direction", shape = "arc",
#' add.alignment.arrows = FALSE
#' )
#' addAnnotation(
#' ggplot.obj = plt, annot.gr = annot.gr, coordinate.space = "self",
#' annotation.level = 0
#' )
#'
plotSelf <- function(paf.table = NULL, min.deletion.size = NULL, min.insertion.size = NULL, highlight.sv = NULL, binsize = NULL, shape = "segment", sort.by = "position", color.by = "direction", color.palette = NULL, add.alignment.arrows = TRUE, highlight.pos = NULL, highlight.region = NULL) {
## Check user input ##
## Make sure submitted paf.table has at least 12 mandatory fields
if (ncol(paf.table) >= 12) {
paf <- paf.table
## Add PAF alignment IDs if it doesn't exists
if (!"aln.id" %in% colnames(paf)) {
paf$aln.id <- seq_len(nrow(paf))
}
} else {
stop("Submitted PAF alignments do not contain a minimum of 12 mandatory fields, see PAF file format definition !!!")
}
## If desired visualization shape is 'arrow' binning is not allowed
if (shape == "arrow" & !is.null(binsize)) {
binsize <- NULL
message("[plotSelf] Binning is not available for shape = 'arrow', setting binsize = NULL.")
}
## Apply self-alignment specific set of filters ##
## Keep only self-alignments (query and target names have to be the same)
paf <- paf[paf$q.name == paf$t.name, ]
if (nrow(paf) == 0) {
stop("No self-alignments present in submitted 'paf.table', self-alignments are expected to have the same value in 'q.name' and 't.name' field !!!")
}
## Remove diagonals (self-alignments) with the same start and end position
paf <- paf[!(paf$q.start == paf$t.start & paf$q.end == paf$t.end), ]
## Due to the minimap2 self-alignment redundancy keep only alignments where query start is smaller than the target start
paf <- paf[paf$q.start < paf$t.start, ]
## Break PAF at insertion/deletions defined in cigar string
if (!is.null(min.deletion.size) | !is.null(min.insertion.size)) {
## Check user input
if (is.null(min.deletion.size)) {
min.deletion.size <- 0
}
if (is.null(min.insertion.size)) {
min.insertion.size <- 0
}
if (min.deletion.size > 0 | min.insertion.size > 0) {
paf.l <- breakPaf(paf.table = paf, min.deletion.size = min.deletion.size, min.insertion.size = min.insertion.size, collapse.mismatches = TRUE, report.sv = TRUE)
paf <- paf.l$M
paf.svs <- paf.l$SVs
}
} else {
paf.svs <- NULL
if (!is.null(highlight.sv)) {
highlight.sv <- NULL
warning("Please specify 'min.deletion.size' and 'min.insertion.size' in order to make parameter 'highlight.sv' to work !!!")
}
}
## Store PAF alignments for later addition of 'geom_gene_arrow'
paf.copy <- paf
paf.copy$ID <- "M"
## Bin PAF alignments
if (!is.null(binsize)) {
if (binsize > 0) {
if (binsize < 10) {
binsize <- 10
warning("Minimum allowed bin size is 10, forced binsize=10!!!")
}
paf <- pafToBins(paf.table = paf, binsize = binsize)
## If the PAF alignments are binned only color.by = 'fraction.matches' is allowed
color.by <- "identity"
}
}
## Mark alignments ranges by 'M' (matches)
paf$ID <- "M"
## Add SVs to the alignment table
if (!is.null(paf.svs)) {
if (nrow(paf.svs) > 0) {
paf.svs$ID <- "INS"
paf.svs$ID[grep(paf.svs$cg, pattern = "D", ignore.case = TRUE)] <- "DEL"
paf <- dplyr::bind_rows(paf, paf.svs)
}
}
## Prepare data for plotting ##
## When dealing with self-alignments query (left-most) sequence is denoted as s1 and target (right-most) sequence is s2
paf <- paf[paf$ID == "M", ]
coords <- data.frame(
s1.start = paf$q.start,
s1.end = paf$q.end,
s2.start = paf$t.start,
s2.end = paf$t.end,
s1.width = (paf$q.end - paf$q.start) + 1,
s2.width = (paf$t.end - paf$t.start) + 1,
seq.name = paste(unique(paf$q.name, paf$t.name), collapse = "_"),
seq.id = "self",
dir = paf$strand,
n.match = paf$n.match,
aln.len = paf$aln.len,
identity = (paf$n.match / paf$aln.len) * 100,
aln.id = paf$aln.id,
stringsAsFactors = FALSE
)
## Add color.by column if defined
if (color.by %in% colnames(paf)) {
coords[, color.by] <- paf[, color.by]
}
## Get max position (for x-axis plotting)
max.pos <- unique(paf$q.len)
## Flip start and end for reverse oriented alignments
coords[coords$dir == "-", ] <- transform(coords[coords$dir == "-", ],
"s2.start" = coords[coords$dir == "-", ]$s2.end,
"s2.end" = coords[coords$dir == "-", ]$s2.start
)
## Sort alignments
if (sort.by == "position") {
## Order alignments by query position
ord.aln.id <- coords %>%
dplyr::group_by(.data$aln.id) %>%
dplyr::summarise(start.id = min(.data$s1.start)) %>%
dplyr::arrange(.data$start.id)
coords$aln.id <- factor(coords$aln.id, levels = ord.aln.id$aln.id)
coords <- coords %>%
dplyr::group_by(.data$aln.id) %>%
dplyr::arrange(.data$s1.start, .by_group = TRUE)
} else if (sort.by == "length") {
## Order alignments by alignment length
coords <- coords %>%
dplyr::group_by(.data$aln.id) %>%
dplyr::mutate(length.id = sum(.data$aln.len)) %>%
dplyr::arrange(dplyr::desc(.data$length.id), .data$s1.start)
} else {
## Order by alignment id
coords <- coords %>% dplyr::arrange(.data$aln.id, .data$s1.start)
}
## Make self-dotplot ##
#######################
## Define color palette for alignment directionality
if (!is.null(color.palette)) {
if (all(c("+", "-") %in% names(color.palette))) {
pal <- color.palette
} else {
pal <- c("-" = "cornflowerblue", "+" = "forestgreen")
warning("User defined 'color.palette' does not contain both '+' and '-' directions, using default values instead!!!")
}
} else {
pal <- c("-" = "cornflowerblue", "+" = "forestgreen")
}
## Define discrete color palettes
if (color.by == "direction") {
coords$col.levels <- factor(coords$dir, levels = c("+", "-"))
} else if (color.by == "identity") {
coords$identity[is.nan(coords$identity) | is.na(coords$identity)] <- 0
## Define color scheme
coords.l <- getColorScheme(data.table = coords, value.field = "identity", breaks = c(90, 95, 99, 99.5, 99.6, 99.7, 99.8, 99.9))
coords <- coords.l$data
coords$identity <- coords$col.levels
colors <- coords.l$colors
} else if (color.by %in% colnames(paf)) {
## Define color scheme
coords.l <- getColorScheme(data.table = coords, value.field = color.by)
coords <- coords.l$data
colors <- coords.l$colors
} else {
color.by <- "direction"
}
## Define plotting coordinates
if (shape == "segment") {
coords$y1 <- 0
coords$y1end <- 0
coords$y2 <- 0
coords$y2end <- 0
for (i in seq_len(nrow(coords))) {
row.df <- coords[i, ]
if (i == 1) {
row.df$y1 <- 1
row.df$y2 <- 1
row.df$y1end <- row.df$s1.width
row.df$y2end <- row.df$s2.width
offset <- max(row.df$y1end, row.df$y2end)
} else {
row.df$y1 <- offset
row.df$y2 <- offset
row.df$y1end <- offset + row.df$s1.width
row.df$y2end <- offset + row.df$s2.width
offset <- max(row.df$y1end, row.df$y2end)
}
coords[i, ] <- row.df
}
## Get polygon coordinates
plt.dir.df <- coords[coords$dir == "+", ]
plt.rev.df <- coords[coords$dir == "-", ]
if (nrow(plt.dir.df) > 0) {
poly.dir.df <- data.frame(
x = c(rbind(plt.dir.df$s1.start, plt.dir.df$s2.start, plt.dir.df$s2.end, plt.dir.df$s1.end)),
# y=c(rbind(plt.dir.df$y1, plt.dir.df$y2, plt.dir.df$y1end, plt.dir.df$y2end)),
y = c(rbind(plt.dir.df$y1, plt.dir.df$y2, plt.dir.df$y2end, plt.dir.df$y1end)),
group = rep(seq_len(nrow(plt.dir.df)), each = 4),
seq.id = plt.dir.df$seq.id,
seq.name = plt.dir.df$seq.name,
col.levels = rep(plt.dir.df$col.levels, each = 4)
)
} else {
poly.dir.df <- data.frame(
x = c(rbind(NaN, NaN, NaN, NaN)),
y = c(rbind(NaN, NaN, NaN, NaN)),
group = rep(1, each = 4),
seq.id = NA,
seq.name = NA,
col.levels = factor(NA, levels(coords$col.levels))
)
}
if (nrow(plt.rev.df) > 0) {
poly.rev.df <- data.frame(
x = c(rbind(plt.rev.df$s1.start, plt.rev.df$s1.end, plt.rev.df$s2.end, plt.rev.df$s2.start)),
y = c(rbind(plt.rev.df$y1, plt.rev.df$y1end, plt.rev.df$y2end, plt.rev.df$y2)),
group = rep(seq_len(nrow(plt.rev.df)), each = 4),
seq.id = plt.rev.df$seq.id,
seq.name = plt.rev.df$seq.name,
col.levels = rep(plt.rev.df$col.levels, each = 4)
)
} else {
poly.rev.df <- data.frame(
x = c(rbind(NaN, NaN, NaN, NaN)),
y = c(rbind(NaN, NaN, NaN, NaN)),
group = rep(1, each = 4),
seq.id = NA,
seq.name = NA,
col.levels = factor(NA, levels(coords$col.levels))
)
}
## Make segment dotplot
y.limit <- max(c(coords$y1end, coords$y2end))
## Plot alignment pairs
plt <- ggplot2::ggplot(coords) +
ggplot2::geom_segment(ggplot2::aes(x = .data$s1.start, xend = .data$s1.end, y = .data$y1, yend = .data$y1end)) +
ggplot2::geom_segment(ggplot2::aes(x = .data$s2.start, xend = .data$s2.end, y = .data$y2, yend = .data$y2end)) +
ggplot2::geom_polygon(data = poly.dir.df, ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, fill = .data$col.levels), alpha = 0.5) +
ggplot2::geom_polygon(data = poly.rev.df, ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, fill = .data$col.levels), alpha = 0.5) +
ggplot2::scale_x_continuous(labels = scales::comma, expand = c(0, 0), limits = c(0, max.pos)) +
# ggplot2::scale_y_continuous(limits = c(-1, y.limit), expand = c(0.1, 0.1)) +
ggplot2::scale_y_continuous(expand = c(0.1, 0.1)) +
# ggplot2::coord_cartesian(xlim = c(0, max.pos)) +
ggplot2::ylab("Self-alignments") +
ggplot2::xlab("Contig position (bp)")
## Define alignment color scheme
if (color.by == "direction") {
plt <- plt + ggplot2::scale_fill_manual(values = pal, drop = FALSE, name = "Alignment\ndirection")
} else {
plt <- plt + ggplot2::scale_fill_manual(values = colors, drop = FALSE, name = eval(color.by))
}
# coord_fixed(ratio = 1) +
## Add indels
if (!is.null(highlight.sv)) {
if (nrow(paf.svs) > 0) {
## Define SV ranges
## Insertions belong to query coordinates and deletions to target coordinates
ins <- paf.svs[paf.svs$ID == "INS", c("q.name", "q.start", "q.end", "ID")]
colnames(ins) <- c("seqnames", "start", "end", "ID")
del <- paf.svs[paf.svs$ID == "DEL", c("t.name", "t.start", "t.end", "ID")]
colnames(del) <- c("seqnames", "start", "end", "ID")
coords.svs <- dplyr::bind_rows(ins, del)
## Add SVs to the plot
if (highlight.sv == "outline") {
plt <- plt + ggnewscale::new_scale_color() +
ggplot2::geom_rect(data = coords.svs, ggplot2::aes(xmin = .data$start, xmax = .data$end, ymin = -Inf, ymax = Inf, color = .data$ID), fill = NA, alpha = 0.5, inherit.aes = FALSE) +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else if (highlight.sv == "fill") {
plt <- plt + ggnewscale::new_scale_fill() + ggnewscale::new_scale_color() +
ggplot2::geom_rect(data = coords.svs, ggplot2::aes(xmin = .data$start, xmax = .data$end, ymin = -Inf, ymax = Inf, fill = .data$ID, color = .data$ID), size = 0.2, alpha = 0.5, inherit.aes = FALSE) +
ggplot2::scale_fill_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class") +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else {
warning("Parameter 'highlight.sv' can only take values 'outline' or 'fill', see function documentation!!!")
}
} else {
message("There are no SVs to highlight. Try to decrease 'min.deletion.size' and 'min.insertion.size' values!!!")
}
}
} else if (shape == "arc") {
## Get arc coordinates
x <- c(rbind(coords$s1.start, coords$s2.start, coords$s1.end, coords$s2.end))
group <- rep(seq_len(nrow(coords)), each = 4)
seq.id <- "self"
seq.name <- unique(coords$seq.name)
col.levels <- rep(coords$col.levels, each = 4)
plt.df <- data.frame(
x = x,
y = 0,
group = group,
seq.id = seq.id,
seq.name = seq.name,
col.levels = col.levels
)
plt <- ggplot2::ggplot(plt.df) +
geom_wide_arc(ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, fill = .data$col.levels), alpha = 0.5) +
ggplot2::scale_x_continuous(labels = scales::comma, expand = c(0, 0), limits = c(0, max.pos)) +
# ggplot2::coord_cartesian(xlim = c(0, max.pos)) +
ggplot2::ylab("Self-alignments") +
ggplot2::xlab("Contig position (bp)")
## Define alignment color scheme
if (color.by == "direction") {
plt <- plt + ggplot2::scale_fill_manual(values = pal, drop = FALSE, name = "Alignment\ndirection")
} else {
plt <- plt + ggplot2::scale_fill_manual(values = colors, drop = FALSE, name = eval(color.by))
}
## Add indels
if (!is.null(highlight.sv)) {
if (nrow(paf.svs) > 0) {
## Define SV ranges
x <- c(rbind(paf.svs$q.start, paf.svs$t.start, paf.svs$q.end, paf.svs$t.end))
group <- rep(seq_len(nrow(paf.svs)), each = 4)
# seq.id <- c(rbind("s1", "s2", "s1", "s2"))
direction <- rep(paf.svs$strand, each = 4)
ID <- rep(paf.svs$ID, each = 4)
svs.df <- data.frame(
x = x,
y = 0,
group = group,
# seq.id = seq.id,
# seq.name = seq.name,
direction = direction,
ID = ID
)
## Add SVs to the plot
if (highlight.sv == "outline") {
plt <- plt + ggnewscale::new_scale_color() +
geom_wide_arc(data = svs.df, ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, color = .data$ID), fill = NA, alpha = 0.5, inherit.aes = FALSE) +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else if (highlight.sv == "fill") {
plt <- plt + ggnewscale::new_scale_fill() + ggnewscale::new_scale_color() +
geom_wide_arc(data = svs.df, ggplot2::aes(x = .data$x, y = .data$y, group = .data$group, fill = .data$ID, color = .data$ID), size = 0.2, alpha = 0.5, inherit.aes = FALSE) +
ggplot2::scale_fill_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class") +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else {
warning("Parameter 'highlight.sv' can only take values 'outline' or 'fill', see function documentation!!!")
}
} else {
message("There are no SVs to highlight. Try to decrease 'min.deletion.size' and 'min.insertion.size' values!!!")
}
}
} else if (shape == "arrow") {
## Do not add alignment arrows if main shape is arrow
add.alignment.arrows <- FALSE
## Make Arrow plot
arrow.df <- data.frame(
xmin = c(coords$s1.start, coords$s2.start),
xmax = c(coords$s1.end, coords$s2.end),
y = as.numeric(coords$aln.id),
col.levels = factor(c(rep("+", nrow(coords)), coords$dir), levels = c("+", "-")), # to make sure s1 is always forward
seq.id = "self",
seq.name = unique(coords$seq.name)
)
arrow.links <- data.frame(
xmin = pmax(coords$s1.start, coords$s1.end),
xmax = pmin(coords$s2.start, coords$s2.end),
y = as.numeric(coords$aln.id)
)
arrow.df$dir <- ifelse(arrow.df$col.levels == "+", 1, 0)
## Make sure start is always smaller than end of the alignment
arrow.df[, c("xmin", "xmax")] <- t(apply(arrow.df[, c("xmin", "xmax")], 1, sort))
## Plot arrows
plt <- ggplot2::ggplot() +
ggplot2::geom_segment(data = arrow.links, aes(x = .data$xmin, xend = .data$xmax, y = .data$y, yend = .data$y), linetype = "solid") +
gggenes::geom_gene_arrow(data = arrow.df, ggplot2::aes(xmin = .data$xmin, xmax = .data$xmax, y = .data$y, forward = .data$dir, fill = .data$col.levels), arrowhead_height = grid::unit(3, "mm")) +
ggplot2::scale_fill_manual(values = pal, name = "Alignment\ndirection") +
ggplot2::scale_x_continuous(labels = scales::comma, expand = c(0, 0), limits = c(0, max.pos)) +
# ggplot2::scale_y_continuous(expand = c(0.1, 0.1)) +
ggplot2::scale_y_continuous(expand = c(grid::unit(0.1, "mm"), grid::unit(0.1, "mm"))) +
# ggplot2::coord_cartesian(xlim = c(0, max.pos)) +
ggplot2::ylab("Self-alignments") +
ggplot2::xlab("Contig position (bp)")
## Add indels
if (!is.null(highlight.sv)) {
if (nrow(paf.svs) > 0) {
## Define SV ranges
## Insertions belong to query coordinates and deletions to target coordinates
ins <- paf.svs[paf.svs$ID == "INS", c("q.name", "q.start", "q.end", "aln.id", "ID")]
colnames(ins) <- c("seqnames", "start", "end", "aln.id", "ID")
del <- paf.svs[paf.svs$ID == "DEL", c("t.name", "t.start", "t.end", "aln.id", "ID")]
colnames(del) <- c("seqnames", "start", "end", "aln.id", "ID")
coords.svs <- dplyr::bind_rows(ins, del)
## Add SVs to the plot
if (highlight.sv == "outline") {
plt <- plt + ggnewscale::new_scale_color() +
geom_roundrect(data = coords.svs, ggplot2::aes(xmin = .data$start, xmax = .data$end, y = aln.id, color = .data$ID), fill = NA, inherit.aes = FALSE, radius = grid::unit(0, "mm")) +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else if (highlight.sv == "fill") {
plt <- plt + ggnewscale::new_scale_fill() + ggnewscale::new_scale_color() +
geom_roundrect(data = coords.svs, ggplot2::aes(xmin = .data$start, xmax = .data$end, y = aln.id, fill = .data$ID, color = .data$ID), size = 0.2, inherit.aes = FALSE, radius = grid::unit(0, "mm")) +
ggplot2::scale_fill_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class") +
ggplot2::scale_color_manual(values = c("DEL" = "firebrick3", "INS" = "dodgerblue3"), name = "SV class")
} else {
warning("Parameter 'highlight.sv' can only take values 'outline' or 'fill', see function documentation!!!")
}
} else {
message("There are no SVs to highlight. Try to decrease 'min.deletion.size' and 'min.insertion.size' values!!!")
}
}
} else {
warning("Paremeter shape can only take values 'segment', 'arc' or 'arrow' !!!")
plt <- ggplot() +
scale_fill_manual(values = pal) +
ylab("Self-alignments") +
xlab("Contig position (bp)") +
theme_minimal() +
theme(
axis.text.y = element_blank(),
axis.ticks.y = element_blank()
)
}
## Add alignment arrows ##
if (add.alignment.arrows) {
arrow.df <- data.frame(
"xmin" = c(rbind(paf.copy$q.start, paf.copy$t.start)),
"xmax" = c(rbind(paf.copy$q.end, paf.copy$t.end)),
"col.levels" = factor(c(rbind("+", paf.copy$strand)), levels = c("+", "-"))
) # to make sure s1 is always forward
arrow.df$dir <- ifelse(arrow.df$col.levels == "+", 1, 0)
## Make sure start is always smaller than end of the alignment
arrow.df[, c("xmin", "xmax")] <- t(apply(arrow.df[, c("xmin", "xmax")], 1, sort))
## Plot arrows
plt <- plt + ggnewscale::new_scale_fill() +
gggenes::geom_gene_arrow(data = arrow.df, ggplot2::aes(xmin = .data$xmin, xmax = .data$xmax, y = 0, forward = .data$dir, fill = .data$col.levels), arrowhead_height = grid::unit(3, "mm")) +
ggplot2::scale_fill_manual(values = pal, name = "Alignment\ndirection")
}
## Highlight user defined positions
if (!is.null(highlight.pos) & is.numeric(highlight.pos)) {
highlight.pos <- highlight.pos[highlight.pos > 0 & highlight.pos <= max.pos]
if (length(highlight.pos) > 0) {
plt <- plt + ggplot2::geom_vline(xintercept = highlight.pos)
}
}
## Highlight user defined region
if (!is.null(highlight.region)) {
highlight.region <- highlight.region[highlight.region$xmin > 0 & highlight.region$xmax <= max.pos, ]
if (nrow(highlight.region) > 0) {
plt <- plt + ggplot2::geom_rect(data = highlight.region, ggplot2::aes(xmin = .data$xmin, xmax = .data$xmax, ymin = 0, ymax = Inf), color = "red", alpha = 0.25)
}
}
## Set the theme
theme_self <- ggplot2::theme(
panel.grid.major = ggplot2::element_blank(),
panel.grid.minor = ggplot2::element_blank(),
panel.background = ggplot2::element_blank(),
axis.line.x = ggplot2::element_line(linewidth = 1),
axis.ticks.x = ggplot2::element_line(linewidth = 1),
axis.ticks.length.x = grid::unit(2, "mm"),
axis.text.y = ggplot2::element_blank(),
axis.ticks.y = ggplot2::element_blank()
)
plt <- plt + theme_self
## Return final plot
return(plt)
}
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