R/manhattanly.R
In sahirbhatnagar/manhattanly: Interactive Q-Q and Manhattan Plots Using 'plotly.js'
Defines functions
manhattanly.manhattanr
manhattanly.default
manhattanly
Documented in
manhattanly
manhattanly.default
manhattanly.manhattanr
#' Creates a plotly manhattan plot
#'
#' Creates an interactive manhattan plot with multiple annotation options
#'
#' @param x Can be an object of class \code{manhattanr} produced by the
#' \code{\link{manhattanr}} function or a \code{data.frame} which must contain
#' at least the following three columns: \itemize{ \item{the chromosome
#' number} \item{genomic base-pair position} \item{a numeric quantity to plot
#' such as a p-value or zscore} }
#' @param col A character vector indicating the colors of each chromosome. If
#' the number of colors specified is less than the number of unique
#' chromosomes, then the elements will be recycled. Can be
#' \href{https://www.rapidtables.com/web/color/RGB_Color.html}{Hex Codes} as
#' well.
#' @param point_size A \code{numeric} indicating the size of the points on the
#' plot. Default is 5
#' @param labelChr A character vector equal to the number of chromosomes
#' specifying the chromosome labels (e.g., \code{c(1:22, "X", "Y", "MT")}).
#' Default is \code{NULL}, meaning that the actual chromosome numbers will be
#' used.
#' @param suggestiveline Where to draw a "suggestive" line. Default is
#' \code{-log10(1e-5)}. Set to \code{FALSE} to disable.
#' @param suggestiveline_color color of "suggestive" line. Only used if
#' \code{suggestiveline} is not set to \code{FALSE}. Default is \code{"blue"}.
#' @param suggestiveline_width Width of \code{suggestiveline}. Default is 1.
#' @param genomewideline Where to draw a "genome-wide sigificant" line. Default
#' \code{-log10(5e-8)}. Set to \code{FALSE} to disable.
#' @param genomewideline_color color of "genome-wide sigificant" line. Only used
#' if \code{genomewideline} is not set to \code{FALSE}. Default is
#' \code{"red"}.
#' @param genomewideline_width Width of \code{genomewideline}. Default is 1.
#' @param highlight A character vector of SNPs in your dataset to highlight.
#' These SNPs should all be in your dataset. Default is \code{NULL} which
#' means that nothing is highlighted.
#' @param highlight_color Color used to highlight points. Only used if
#' \code{highlight} argument has been specified
#' @param showlegend Should a legend be shown. Default is \code{FALSE}.
#' @param showgrid Should gridlines be shown. Default is \code{FALSE}.
#' @param xlab X-axis label. Default is \code{NULL} which means that the label
#' is automatically determined by the \code{\link{manhattanr}} function.
#' Specify here to overwrite the default.
#' @param ylab Y-axis label. Default is \code{"-log10(p)"}.
#' @param title Title of the plot. Default is \code{"Manhattan Plot"}
#' @param ... other parameters passed to \code{\link{manhattanr}}
#' @note This package is inspired by the
#' \href{https://github.com/stephenturner/qqman}{\code{qqman}} package. This
#' package provides additional annotation options and builds on the
#' \code{\link{plotly}} \code{d3.js} engine. These plots can be included in
#' Dash apps, Shiny apps, Rmarkdown documents or embedded in websites using
#' simple HTML code.
#' @return An interactive manhattan plot.
#' @seealso \code{\link{manhattanr}}, \code{\link{HapMap}},
#' \code{\link{significantSNP}}
#' @aliases manhattanly.default manhattanly.manhattanr
#' @importFrom magrittr '%<>%'
#' @export
#' @examples
#' \dontrun{
#' library(manhattanly)
#' manhattanly(HapMap)
#'
#' # highlight SNPs of interest
#' # 'signigicantSNP' is a character vector of SNPs included in this package
#' manhattanly(HapMap, snp = "SNP", highlight = significantSNP)
#' }
manhattanly <- function(x,
...,
col = c("#969696", "#252525"),
point_size = 5,
labelChr = NULL,
suggestiveline = -log10(1e-5),
suggestiveline_color = "blue",
suggestiveline_width = 1,
genomewideline = -log10(5e-8),
genomewideline_color = "red",
genomewideline_width = 1,
highlight = NULL,
highlight_color = "#00FF00",
showlegend = FALSE,
showgrid = FALSE,
xlab = NULL,
ylab = "-log10(p)",
title = "Manhattan Plot") {
UseMethod("manhattanly")
}
#' @export
manhattanly.default <- function(x,
...,
col = c("#969696", "#252525"),
point_size = 5,
labelChr = NULL,
suggestiveline = -log10(1e-5),
suggestiveline_color = "blue",
suggestiveline_width = 1,
genomewideline = -log10(5e-8),
genomewideline_color = "red",
genomewideline_width = 1,
highlight = NULL,
highlight_color = "#00FF00",
showlegend = FALSE,
showgrid = FALSE,
xlab = NULL,
ylab = "-log10(p)",
title = "Manhattan Plot") {
mh <- manhattanr(x, ...)
nchr <- mh$nchr
manhattanly.manhattanr(mh,
col = col,
labelChr = labelChr,
point_size = point_size,
suggestiveline = suggestiveline,
suggestiveline_color = suggestiveline_color,
suggestiveline_width = suggestiveline_width,
genomewideline = genomewideline,
genomewideline_color = genomewideline_color,
genomewideline_width = genomewideline_width,
highlight = highlight,
highlight_color = highlight_color,
showlegend = showlegend,
showgrid = showgrid,
xlab = xlab,
ylab = ylab,
title = title)
}
#' @export
manhattanly.manhattanr <- function(x,
...,
col = c("#969696", "#252525"),
point_size = 5,
labelChr = NULL,
suggestiveline = -log10(1e-5),
suggestiveline_color = "blue",
suggestiveline_width = 1,
genomewideline = -log10(5e-8),
genomewideline_color = "red",
genomewideline_width = 1,
highlight = NULL,
highlight_color = "#00FF00",
showlegend = FALSE,
showgrid = FALSE,
xlab = NULL,
ylab = "-log10(p)",
title = "Manhattan Plot") {
d <- x$data
snpName <- x$snpName
geneName <- x$geneName
annotation1Name <- x$annotation1Name
annotation2Name <- x$annotation2Name
labs <- x$labs
xlabel <- x$xlabel
ticks <- x$ticks
nchr <- x$nchr
if (!is.null(highlight) & is.na(snpName)) stop("You're trying to highlight snps, but havent provided a snp column")
# Initialize plot
xmax <- ceiling(max(d$pos) * 1.03)
xmin <- floor(max(d$pos) * -0.03)
# If manually specifying chromosome labels, ensure a character vector
# and number of labels matches number chrs.
if (!is.null(labelChr)) {
if (is.character(labelChr)) {
if (length(labelChr)==length(labs)) {
labs <- labelChr
} else {
warning("You're trying to specify chromosome labels but the number of labels != number of chromosomes.")
}
} else {
warning("If you're trying to specify chromosome labels, labelChr must be a character vector")
}
}
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Initalize plotly
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
p <- plotly::plot_ly()
# Add an axis.
if (nchr == 1) {
# If single chromosome, ticks and labels automatic.
p %<>% plotly::layout(p,
title = title,
xaxis = list(
title = if(!is.null(xlab)) xlab else xlabel,
# title = "ll",
showgrid = showgrid,
range = c(xmin, xmax)
),
yaxis = list(
title = ylab)
)
} else {
# if multiple chrs, use the ticks and labels you created above.
p %<>% plotly::layout(p,
title = title,
xaxis = list(
title = if(!is.null(xlab)) xlab else "Chromosome",
# title = "ll",
showgrid = showgrid,
range = c(xmin, xmax),
autotick = FALSE,
tickmode = "array",
tickvals = ticks,
ticktext = labs,
ticks = "outside"
),
yaxis = list(
title = ylab)
)
}
# Create a vector of alternatiting colors
col <- rep(col, max(d$CHR))
# Add points to the plot
if (nchr==1) {
TEXT <- paste(if (!is.na(snpName)) paste0(snpName,": ",d[[snpName]]),
if (!is.na(geneName)) paste0(geneName,": ",d[[geneName]]),
if (!is.na(annotation1Name)) paste0(annotation1Name,": ",d[[annotation1Name]]),
if (!is.na(annotation2Name)) paste0(annotation2Name,": ",d[[annotation2Name]]), sep = "<br>")
if (is.na(snpName) && is.na(geneName) && is.na(annotation1Name) && is.na(annotation2Name)) {
p %<>% plotly::add_trace(x = d$pos, y = d$logp,
type = "scatter",
mode = "markers",
# text = TEXT,
showlegend = showlegend,
marker = list(color = col[1],
size = point_size),
name = paste0("chr", unique(d$CHR)))
} else {
p %<>% plotly::add_trace(x = d$pos, y = d$logp,
type = "scatter",
mode = "markers",
text = TEXT,
showlegend = showlegend,
marker = list(color = col[1],
size = point_size),
name = paste0("chr", unique(d$CHR)))
}
} else {
icol <- 1
for(i in unique(d$index)) {
tmp <- d[d$index == unique(d$index)[i], ]
TEXT <- paste(if (!is.na(snpName)) paste0(snpName,": ", tmp[[snpName]]),
if (!is.na(geneName)) paste0(geneName,": ", tmp[[geneName]]),
if (!is.na(annotation1Name)) paste0(annotation1Name,": ", tmp[[annotation1Name]]),
if (!is.na(annotation2Name)) paste0(annotation2Name,": ", tmp[[annotation2Name]]),
sep = "<br>")
# get chromosome name for labeling
chromo <- unique(tmp[which(tmp$index==i),"CHR"])
if (is.na(snpName) && is.na(geneName) && is.na(annotation1Name) && is.na(annotation2Name)) {
p %<>% plotly::add_trace(x = tmp$pos, y = tmp$logp, type = "scatter",
mode = "markers",
showlegend = showlegend,
marker = list(color = col[icol],
size = point_size),
name = paste0("chr",chromo))
} else {
p %<>% plotly::add_trace(x = tmp$pos, y = tmp$logp, type = "scatter",
mode = "markers",
showlegend = showlegend,
text = TEXT,
marker = list(color = col[icol],
size = point_size),
name = paste0("chr",chromo))
}
icol = icol + 1
}
}
if (suggestiveline & genomewideline) {p %<>% plotly::layout(p,
shapes = list(
list(type = "line",
fillcolor = suggestiveline_color,
line = list(color = suggestiveline_color,
width = suggestiveline_width),
x0 = xmin, x1 = xmax, xref = "x",
y0 = suggestiveline, y1 = suggestiveline, yref = "y"),
list(type = "line",
fillcolor = genomewideline_color,
line = list(color = genomewideline_color,
width = genomewideline_width),
x0 = xmin, x1 = xmax, xref = "x",
y0 = genomewideline, y1 = genomewideline, yref = "y")
))}
if (suggestiveline & !(genomewideline)) {p %<>% plotly::layout(p,
shapes = list(
list(type = "line",
fillcolor = suggestiveline_color,
line = list(color = suggestiveline_color,
width = suggestiveline_width),
x0 = xmin, x1 = xmax, xref = "x",
y0 = suggestiveline, y1 = suggestiveline, yref = "y")
))}
if (!(suggestiveline) & genomewideline) {p %<>% plotly::layout(p,
shapes = list(
list(type = "line",
fillcolor = genomewideline_color,
line = list(color = genomewideline_color,
width = genomewideline_width),
x0 = xmin, x1 = xmax, xref = "x",
y0 = genomewideline, y1 = genomewideline, yref = "y")
))}
# Highlight snps from a character vector
if (!is.na(snpName)) {
if (!is.null(highlight)) {
if (any(!(highlight %in% d[[snpName]]))) warning("You're trying to highlight SNPs that don't exist in your results.")
d.highlight <- d[which(d[[snpName]] %in% highlight), ]
# Add points to the plot
if (nchr==1) {
TEXT <- paste(if (!is.na(snpName)) paste0(snpName,": ",d.highlight[[snpName]]),
if (!is.na(geneName)) paste0(geneName,": ",d.highlight[[geneName]]),
if (!is.na(annotation1Name)) paste0(annotation1Name,": ",d.highlight[[annotation1Name]]),
if (!is.na(annotation2Name)) paste0(annotation2Name,": ",d.highlight[[annotation2Name]]), sep = "<br>")
p %<>% plotly::add_trace(x = d.highlight$pos, y = d.highlight$logp,
type = "scatter",
mode = "markers",
text = TEXT,
showlegend = showlegend,
marker = list(color = highlight_color,
size = point_size),
name = "of interest")
} else {
for(i in unique(d.highlight$index)) {
tmp <- d.highlight[d.highlight$index == i, ]
TEXT <- paste(if (!is.na(snpName)) paste0(snpName,": ", tmp[[snpName]]),
if (!is.na(geneName)) paste0(geneName,": ", tmp[[geneName]]),
if (!is.na(annotation1Name)) paste0(annotation1Name,": ", tmp[[annotation1Name]]),
if (!is.na(annotation2Name)) paste0(annotation2Name,": ", tmp[[annotation2Name]]),
sep = "<br>")
# get chromosome name for labeling
chromo <- unique(tmp[which(tmp$index==i),"CHR"])
p %<>% plotly::add_trace(x = tmp$pos,
y = tmp$logp,
type = "scatter",
mode = "markers",
text = TEXT,
showlegend = showlegend,
marker = list(color = highlight_color,
size = point_size),
name = "of interest")
}
}
}
}
p
}
sahirbhatnagar/manhattanly documentation built on May 1, 2021, 10:01 p.m.
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Defines functions manhattanly.manhattanr manhattanly.default manhattanly
Documented in manhattanly manhattanly.default manhattanly.manhattanr
#' Creates a plotly manhattan plot
#'
#' Creates an interactive manhattan plot with multiple annotation options
#'
#' @param x Can be an object of class \code{manhattanr} produced by the
#' \code{\link{manhattanr}} function or a \code{data.frame} which must contain
#' at least the following three columns: \itemize{ \item{the chromosome
#' number} \item{genomic base-pair position} \item{a numeric quantity to plot
#' such as a p-value or zscore} }
#' @param col A character vector indicating the colors of each chromosome. If
#' the number of colors specified is less than the number of unique
#' chromosomes, then the elements will be recycled. Can be
#' \href{https://www.rapidtables.com/web/color/RGB_Color.html}{Hex Codes} as
#' well.
#' @param point_size A \code{numeric} indicating the size of the points on the
#' plot. Default is 5
#' @param labelChr A character vector equal to the number of chromosomes
#' specifying the chromosome labels (e.g., \code{c(1:22, "X", "Y", "MT")}).
#' Default is \code{NULL}, meaning that the actual chromosome numbers will be
#' used.
#' @param suggestiveline Where to draw a "suggestive" line. Default is
#' \code{-log10(1e-5)}. Set to \code{FALSE} to disable.
#' @param suggestiveline_color color of "suggestive" line. Only used if
#' \code{suggestiveline} is not set to \code{FALSE}. Default is \code{"blue"}.
#' @param suggestiveline_width Width of \code{suggestiveline}. Default is 1.
#' @param genomewideline Where to draw a "genome-wide sigificant" line. Default
#' \code{-log10(5e-8)}. Set to \code{FALSE} to disable.
#' @param genomewideline_color color of "genome-wide sigificant" line. Only used
#' if \code{genomewideline} is not set to \code{FALSE}. Default is
#' \code{"red"}.
#' @param genomewideline_width Width of \code{genomewideline}. Default is 1.
#' @param highlight A character vector of SNPs in your dataset to highlight.
#' These SNPs should all be in your dataset. Default is \code{NULL} which
#' means that nothing is highlighted.
#' @param highlight_color Color used to highlight points. Only used if
#' \code{highlight} argument has been specified
#' @param showlegend Should a legend be shown. Default is \code{FALSE}.
#' @param showgrid Should gridlines be shown. Default is \code{FALSE}.
#' @param xlab X-axis label. Default is \code{NULL} which means that the label
#' is automatically determined by the \code{\link{manhattanr}} function.
#' Specify here to overwrite the default.
#' @param ylab Y-axis label. Default is \code{"-log10(p)"}.
#' @param title Title of the plot. Default is \code{"Manhattan Plot"}
#' @param ... other parameters passed to \code{\link{manhattanr}}
#' @note This package is inspired by the
#' \href{https://github.com/stephenturner/qqman}{\code{qqman}} package. This
#' package provides additional annotation options and builds on the
#' \code{\link{plotly}} \code{d3.js} engine. These plots can be included in
#' Dash apps, Shiny apps, Rmarkdown documents or embedded in websites using
#' simple HTML code.
#' @return An interactive manhattan plot.
#' @seealso \code{\link{manhattanr}}, \code{\link{HapMap}},
#' \code{\link{significantSNP}}
#' @aliases manhattanly.default manhattanly.manhattanr
#' @importFrom magrittr '%<>%'
#' @export
#' @examples
#' \dontrun{
#' library(manhattanly)
#' manhattanly(HapMap)
#'
#' # highlight SNPs of interest
#' # 'signigicantSNP' is a character vector of SNPs included in this package
#' manhattanly(HapMap, snp = "SNP", highlight = significantSNP)
#' }
manhattanly <- function(x,
...,
col = c("#969696", "#252525"),
point_size = 5,
labelChr = NULL,
suggestiveline = -log10(1e-5),
suggestiveline_color = "blue",
suggestiveline_width = 1,
genomewideline = -log10(5e-8),
genomewideline_color = "red",
genomewideline_width = 1,
highlight = NULL,
highlight_color = "#00FF00",
showlegend = FALSE,
showgrid = FALSE,
xlab = NULL,
ylab = "-log10(p)",
title = "Manhattan Plot") {
UseMethod("manhattanly")
}
#' @export
manhattanly.default <- function(x,
...,
col = c("#969696", "#252525"),
point_size = 5,
labelChr = NULL,
suggestiveline = -log10(1e-5),
suggestiveline_color = "blue",
suggestiveline_width = 1,
genomewideline = -log10(5e-8),
genomewideline_color = "red",
genomewideline_width = 1,
highlight = NULL,
highlight_color = "#00FF00",
showlegend = FALSE,
showgrid = FALSE,
xlab = NULL,
ylab = "-log10(p)",
title = "Manhattan Plot") {
mh <- manhattanr(x, ...)
nchr <- mh$nchr
manhattanly.manhattanr(mh,
col = col,
labelChr = labelChr,
point_size = point_size,
suggestiveline = suggestiveline,
suggestiveline_color = suggestiveline_color,
suggestiveline_width = suggestiveline_width,
genomewideline = genomewideline,
genomewideline_color = genomewideline_color,
genomewideline_width = genomewideline_width,
highlight = highlight,
highlight_color = highlight_color,
showlegend = showlegend,
showgrid = showgrid,
xlab = xlab,
ylab = ylab,
title = title)
}
#' @export
manhattanly.manhattanr <- function(x,
...,
col = c("#969696", "#252525"),
point_size = 5,
labelChr = NULL,
suggestiveline = -log10(1e-5),
suggestiveline_color = "blue",
suggestiveline_width = 1,
genomewideline = -log10(5e-8),
genomewideline_color = "red",
genomewideline_width = 1,
highlight = NULL,
highlight_color = "#00FF00",
showlegend = FALSE,
showgrid = FALSE,
xlab = NULL,
ylab = "-log10(p)",
title = "Manhattan Plot") {
d <- x$data
snpName <- x$snpName
geneName <- x$geneName
annotation1Name <- x$annotation1Name
annotation2Name <- x$annotation2Name
labs <- x$labs
xlabel <- x$xlabel
ticks <- x$ticks
nchr <- x$nchr
if (!is.null(highlight) & is.na(snpName)) stop("You're trying to highlight snps, but havent provided a snp column")
# Initialize plot
xmax <- ceiling(max(d$pos) * 1.03)
xmin <- floor(max(d$pos) * -0.03)
# If manually specifying chromosome labels, ensure a character vector
# and number of labels matches number chrs.
if (!is.null(labelChr)) {
if (is.character(labelChr)) {
if (length(labelChr)==length(labs)) {
labs <- labelChr
} else {
warning("You're trying to specify chromosome labels but the number of labels != number of chromosomes.")
}
} else {
warning("If you're trying to specify chromosome labels, labelChr must be a character vector")
}
}
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Initalize plotly
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
p <- plotly::plot_ly()
# Add an axis.
if (nchr == 1) {
# If single chromosome, ticks and labels automatic.
p %<>% plotly::layout(p,
title = title,
xaxis = list(
title = if(!is.null(xlab)) xlab else xlabel,
# title = "ll",
showgrid = showgrid,
range = c(xmin, xmax)
),
yaxis = list(
title = ylab)
)
} else {
# if multiple chrs, use the ticks and labels you created above.
p %<>% plotly::layout(p,
title = title,
xaxis = list(
title = if(!is.null(xlab)) xlab else "Chromosome",
# title = "ll",
showgrid = showgrid,
range = c(xmin, xmax),
autotick = FALSE,
tickmode = "array",
tickvals = ticks,
ticktext = labs,
ticks = "outside"
),
yaxis = list(
title = ylab)
)
}
# Create a vector of alternatiting colors
col <- rep(col, max(d$CHR))
# Add points to the plot
if (nchr==1) {
TEXT <- paste(if (!is.na(snpName)) paste0(snpName,": ",d[[snpName]]),
if (!is.na(geneName)) paste0(geneName,": ",d[[geneName]]),
if (!is.na(annotation1Name)) paste0(annotation1Name,": ",d[[annotation1Name]]),
if (!is.na(annotation2Name)) paste0(annotation2Name,": ",d[[annotation2Name]]), sep = "<br>")
if (is.na(snpName) && is.na(geneName) && is.na(annotation1Name) && is.na(annotation2Name)) {
p %<>% plotly::add_trace(x = d$pos, y = d$logp,
type = "scatter",
mode = "markers",
# text = TEXT,
showlegend = showlegend,
marker = list(color = col[1],
size = point_size),
name = paste0("chr", unique(d$CHR)))
} else {
p %<>% plotly::add_trace(x = d$pos, y = d$logp,
type = "scatter",
mode = "markers",
text = TEXT,
showlegend = showlegend,
marker = list(color = col[1],
size = point_size),
name = paste0("chr", unique(d$CHR)))
}
} else {
icol <- 1
for(i in unique(d$index)) {
tmp <- d[d$index == unique(d$index)[i], ]
TEXT <- paste(if (!is.na(snpName)) paste0(snpName,": ", tmp[[snpName]]),
if (!is.na(geneName)) paste0(geneName,": ", tmp[[geneName]]),
if (!is.na(annotation1Name)) paste0(annotation1Name,": ", tmp[[annotation1Name]]),
if (!is.na(annotation2Name)) paste0(annotation2Name,": ", tmp[[annotation2Name]]),
sep = "<br>")
# get chromosome name for labeling
chromo <- unique(tmp[which(tmp$index==i),"CHR"])
if (is.na(snpName) && is.na(geneName) && is.na(annotation1Name) && is.na(annotation2Name)) {
p %<>% plotly::add_trace(x = tmp$pos, y = tmp$logp, type = "scatter",
mode = "markers",
showlegend = showlegend,
marker = list(color = col[icol],
size = point_size),
name = paste0("chr",chromo))
} else {
p %<>% plotly::add_trace(x = tmp$pos, y = tmp$logp, type = "scatter",
mode = "markers",
showlegend = showlegend,
text = TEXT,
marker = list(color = col[icol],
size = point_size),
name = paste0("chr",chromo))
}
icol = icol + 1
}
}
if (suggestiveline & genomewideline) {p %<>% plotly::layout(p,
shapes = list(
list(type = "line",
fillcolor = suggestiveline_color,
line = list(color = suggestiveline_color,
width = suggestiveline_width),
x0 = xmin, x1 = xmax, xref = "x",
y0 = suggestiveline, y1 = suggestiveline, yref = "y"),
list(type = "line",
fillcolor = genomewideline_color,
line = list(color = genomewideline_color,
width = genomewideline_width),
x0 = xmin, x1 = xmax, xref = "x",
y0 = genomewideline, y1 = genomewideline, yref = "y")
))}
if (suggestiveline & !(genomewideline)) {p %<>% plotly::layout(p,
shapes = list(
list(type = "line",
fillcolor = suggestiveline_color,
line = list(color = suggestiveline_color,
width = suggestiveline_width),
x0 = xmin, x1 = xmax, xref = "x",
y0 = suggestiveline, y1 = suggestiveline, yref = "y")
))}
if (!(suggestiveline) & genomewideline) {p %<>% plotly::layout(p,
shapes = list(
list(type = "line",
fillcolor = genomewideline_color,
line = list(color = genomewideline_color,
width = genomewideline_width),
x0 = xmin, x1 = xmax, xref = "x",
y0 = genomewideline, y1 = genomewideline, yref = "y")
))}
# Highlight snps from a character vector
if (!is.na(snpName)) {
if (!is.null(highlight)) {
if (any(!(highlight %in% d[[snpName]]))) warning("You're trying to highlight SNPs that don't exist in your results.")
d.highlight <- d[which(d[[snpName]] %in% highlight), ]
# Add points to the plot
if (nchr==1) {
TEXT <- paste(if (!is.na(snpName)) paste0(snpName,": ",d.highlight[[snpName]]),
if (!is.na(geneName)) paste0(geneName,": ",d.highlight[[geneName]]),
if (!is.na(annotation1Name)) paste0(annotation1Name,": ",d.highlight[[annotation1Name]]),
if (!is.na(annotation2Name)) paste0(annotation2Name,": ",d.highlight[[annotation2Name]]), sep = "<br>")
p %<>% plotly::add_trace(x = d.highlight$pos, y = d.highlight$logp,
type = "scatter",
mode = "markers",
text = TEXT,
showlegend = showlegend,
marker = list(color = highlight_color,
size = point_size),
name = "of interest")
} else {
for(i in unique(d.highlight$index)) {
tmp <- d.highlight[d.highlight$index == i, ]
TEXT <- paste(if (!is.na(snpName)) paste0(snpName,": ", tmp[[snpName]]),
if (!is.na(geneName)) paste0(geneName,": ", tmp[[geneName]]),
if (!is.na(annotation1Name)) paste0(annotation1Name,": ", tmp[[annotation1Name]]),
if (!is.na(annotation2Name)) paste0(annotation2Name,": ", tmp[[annotation2Name]]),
sep = "<br>")
# get chromosome name for labeling
chromo <- unique(tmp[which(tmp$index==i),"CHR"])
p %<>% plotly::add_trace(x = tmp$pos,
y = tmp$logp,
type = "scatter",
mode = "markers",
text = TEXT,
showlegend = showlegend,
marker = list(color = highlight_color,
size = point_size),
name = "of interest")
}
}
}
}
p
}
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