R/genetrack_ly.R

In locuszoomr: Gene Locus Plot with Gene Annotations

#' Gene tracks using 'plotly'
#' 
#' Plot gene annotation tracks from `ensembldb` data using `plotly`.
#' 
#' @details This function can used to plot gene annotation tracks on their own.
#' @param locus Object of class 'locus' generated by [locus()].
#' @param filter_gene_name Vector of gene names to display.
#' @param filter_gene_biotype Vector of gene biotypes to be filtered. Use
#' [ensembldb::listGenebiotypes()] to display possible biotypes. For example, 
#' `ensembldb::listGenebiotypes(EnsDb.Hsapiens.v75)`
#' @param cex.text Font size for gene text.
#' @param italics Logical whether gene text is in italics.
#' @param gene_col Colour for gene lines.
#' @param exon_col Fill colour for exons.
#' @param exon_border Border line colour outlining exons (or genes if
#'   `showExons` is `FALSE`). Set to `NA` for no border.
#' @param showExons Logical whether to show exons or simply show whole gene as a
#'   rectangle. If `showExons = FALSE` colours are specified by `exon_border`
#'   for rectangle border and `gene_col` for the fill colour.
#' @param maxrows Specifies maximum number of rows to display in gene 
#' annotation panel.
#' @param width Width of plotly plot in pixels which is purely used to prevent
#'   overlapping text for gene names.
#' @param xlab Title for x axis. Defaults to chromosome `seqname` specified 
#' in `locus`.
#' @param blanks Controls handling of genes with blank names: `"fill"` replaces
#'   blank gene symbols with ensembl gene ids. `"hide"` completely hides genes
#'   which are missing gene symbols. `"show"` shows gene lines but no label
#'   (hovertext is still available).
#' @param height Height in pixels (optional, defaults to automatic sizing).
#' @param plot Logical whether to produce plotly object or return plot
#'   coordinates.
#' @return Either a 'plotly' plotting object showing gene tracks, or if 
#'   `plot = FALSE` a list containing `TX`, a dataframe of coordinates for
#'   gene transcripts, and `EX`, a dataframe of coordinates for exons.
#' @examples
#' if(require(EnsDb.Hsapiens.v75)) {
#' data(SLE_gwas_sub)
#' loc <- locus(SLE_gwas_sub, gene = 'UBE2L3', flank = 1e5,
#'              ens_db = "EnsDb.Hsapiens.v75")
#' genetrack_ly(loc)
#' }
#' @importFrom plotly plot_ly plotly_empty add_segments add_text %>%
#' @export

genetrack_ly <- function(locus,
                         filter_gene_name = NULL,
                         filter_gene_biotype = NULL,
                         cex.text = 0.7,
                         italics = FALSE,
                         gene_col = ifelse(showExons, 'blue4', 'skyblue'),
                         exon_col = 'blue4',
                         exon_border = 'blue4',
                         showExons = TRUE,
                         maxrows = 8,
                         width = 600,
                         xlab = NULL,
                         blanks = c("fill", "hide", "show"),
                         height = NULL,
                         plot = TRUE) {
  if (!inherits(locus, "locus")) stop("Object of class 'locus' required")
  blanks <- match.arg(blanks)
  TX <- locus$TX
  EX <- as.data.frame(locus$EX)
  xrange <- locus$xrange
  if (!is.null(filter_gene_name)) {
    TX <- TX[TX$gene_name %in% filter_gene_name, ]
  }
  if (!is.null(filter_gene_biotype)) {
    TX <- TX[TX$gene_biotype %in% filter_gene_biotype, ]
  }
  xlim <- xrange / 1e6
  xext <- diff(xlim) * 0.01
  xlim <- xlim + c(-xext, xext)
  if (is.null(xlab)) xlab <- paste("Chromosome", locus$seqname, "(Mb)")
  if (nrow(TX) == 0 & plot) {
    message('No genes to plot')
    # blank gene tracks
    p <- plot_ly(data.frame(NA), mode = "markers", type = "scatter",
                 source = "plotly_locus") %>%
      plotly::layout(xaxis = list(title = xlab, showgrid = FALSE, showline = TRUE,
                                  color = 'black', ticklen = 5,
                                  range = as.list(xlim)),
                     yaxis = list(title = "", showgrid = FALSE, zeroline = FALSE,
                                  showticklabels = FALSE)) %>%
      plotly::config(displaylogo = FALSE)
    return(p)
  }
  
  cex.width <- cex.text * par("pin")[1] * 80 / (width - 250)
  TX <- mapRow(TX, xlim = xrange, cex.text = cex.width, blanks = blanks)
  maxrows <- if (is.null(maxrows)) max(TX$row) else min(c(max(TX$row), maxrows))
  if (max(TX$row) > maxrows) message(max(TX$row), " tracks needed to show all genes")
  TX <- TX[TX$row <= maxrows, ]
  EX <- EX[EX$gene_id %in% TX$gene_id, ]
  
  gene_col <- col2hex(gene_col)
  exon_col <- col2hex(exon_col)
  exon_border <- col2hex(exon_border)
  EX$row <- TX$row[match(EX$gene_id, TX$gene_id)]
  
  EX[, c('start', 'end')] <- EX[, c('start', 'end')] / 1e6
  TX$tx <- rowMeans(TX[, c('start', 'end')])
  TX$ty <- -TX$row + 0.35
  TX[, c('start', 'end', 'tx')] <- TX[, c('start', 'end', 'tx')] / 1e6
  
  tfilter <- TX$tmin > (xrange[1] - diff(xrange) * 0.005) & 
             (TX$tmax < xrange[2] + diff(xrange) * 0.005) &
             TX$gene_name != ""
  pos <- TX$strand == "+"
  TX$gene_name2 <- if (italics) paste0("<i>", TX$gene_name, "</i>") else TX$gene_name
  TX$gene_name2[pos] <- paste0(TX$gene_name2[pos], "&#8594;")
  TX$gene_name2[!pos] <- paste0("&#8592;", TX$gene_name2[!pos])
  TX$gene_name2[!tfilter] <- NA
  
  if (!plot) return(list(TX = TX, EX = EX))
  
  if (showExons) {
    shapes <- lapply(seq_len(nrow(EX)), function(i) {
      list(type = "rect", fillcolor = exon_col, line = list(color = exon_border,
                                                            width = 0.5),
           x0 = EX$start[i], x1 = EX$end[i], xref = "x",
           y0 = -EX$row[i] - 0.15, y1 = -EX$row[i] + 0.15, yref = "y")
    })
  } else {
    shapes <- lapply(seq_len(nrow(TX)), function(i) {
      list(type = "rect", fillcolor = gene_col, line = list(color = exon_border,
                                                            width = 1),
           x0 = TX$start[i], x1 = TX$end[i], xref = "x",
           y0 = -TX$row[i] - 0.15, y1 = -TX$row[i] + 0.15, yref = "y")
    })
  }
  
  ok <- !is.na(TX$gene_name2)
  hovertext <- paste0(TX$gene_name,
                      TX$fullname,
                      "<br>Gene ID: ", TX$gene_id,
                      "<br>Biotype: ", TX$gene_biotype,
                      "<br>Start: ", TX$start * 1e6,
                      "<br>End: ", TX$end * 1e6)
  plot_ly(TX, source = "plotly_locus", height = height) %>%
    add_segments(x = ~start, y = ~-row,
                 xend = ~end, yend = ~-row,
                 color = I(gene_col),
                 text = hovertext, hoverinfo = 'text',
                 showlegend = FALSE) %>%
    add_text(x = TX$tx[ok], y = TX$ty[ok], text = TX$gene_name2[ok],
             textfont = list(size = 14 * cex.text),
             showlegend = FALSE, hoverinfo = 'none') %>%
    plotly::layout(shapes = shapes,
                   xaxis = list(title = xlab, showgrid = FALSE, showline = TRUE,
                                zeroline = FALSE,
                                color = 'black', ticklen = 5,
                                range = as.list(xlim)),
                   yaxis = list(title = "", showgrid = FALSE, zeroline = FALSE,
                                fixedrange = TRUE,
                                showticklabels = FALSE),
                   showlegend = TRUE, dragmode = "pan") %>%
    plotly::config(displaylogo = FALSE,
                   modeBarButtonsToRemove = c("select2d", "lasso2d",
                                              "autoScale2d", "resetScale2d",
                                              "hoverClosest", "hoverCompare"))
}


#' @importFrom grDevices col2rgb rgb

col2hex <- function(cname) {
  colMat <- col2rgb(cname)
  rgb(red = colMat[1, ]/255, green = colMat[2, ]/255, blue = colMat[3, ]/255)
}