v0.1

DESCRIPTION

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+Package: g3viz
+Type: Package
+Title: visulize MAF genomic annotation data
+Version: 0.1.0
+Author: person("Xin", "Guo", email = "[email protected]", role=c("aut", "cre"))
+Description: a warpper of g3viz javascript library to generate interactive "lollipop-style" diagram to visualize mutation data
+License: MIT
+Encoding: UTF-8
+LazyData: true
+Depends:
+    R (>= 3.0.2)
+Imports:
+    jsonlite
+Suggests:
+    shiny (>= 1.0.0),
+    httpuv (>= 1.4.0)
+URL: https://github.com/G3js/G3vizr
+BugReports: https://github.com/G3js/G3vizr/issues
+RoxygenNote: 6.0.1

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(formatCamelCase)
+export(g3Lollipop)
+export(g3LollipopOutput)
+export(getDefaultMutationMappingTable)
+export(getMutationsFromCbioportal)
+export(hgnc2pfam)
+export(hgnc2uniprot)
+export(mapMutationTypeToMutationClass)
+export(parseProteinChange)
+export(readMAF)
+export(renderG3Lollipop)
+export(uniprot2pfam)
+import(cgdsr)
+import(htmlwidgets)

R/formatCamelCase.R

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+#' change to camel case
+#' @export
+formatCamelCase <- function(in.df){
+  stopifnot(is.data.frame(in.df))
+
+  firstLetterCap <- function(x, sep = "_") {
+    s <- strsplit(x, sep)[[1]]
+    paste(toupper(substring(s, 1,1)), substring(s, 2), sep = "", collapse = sep)
+  }
+
+  col.names <- colnames(in.df)
+  col.new.names <- sapply(col.names, firstLetterCap)
+  colnames(in.df) <- col.new.names
+
+  in.df
+}

R/g3Lollipop.R

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+#' Plot Lollipop diagram plot for mutation data.
+#'
+#' @description
+#'
+#' @param mutation.dat Mutation data frame.
+#' @param gene.symbol HGNC gene symbol.
+#' @param gene.symbol.col Column name of Hugo gene symbols (e.g., TP53). Default \emph{Hugo_Symbol}.
+#' @param variant.class.col Column name of variant class information
+#' (e.g., \emph{Missense_Mutation}, \emph{Nonsense_Mutation}). Default \emph{Variant_Classification}.
+#' @param protein.change.col Column name of protein change information (e.g., p.K960R, G658S, L14Sfs*15).
+#' Default \emph{Protein_Change}.
+#' @param mutation.class.col Column name of the parsed mutation class. Default \emph{Mutation_Class}.
+#' @param aachange.pos.col Column name of the parsed amino-acid change position. Default \emph{AA_Position}.
+#' @param factor.col column of classes in the plot legend. IF \code{NA}, use parsed \emph{Mutation_Class} column,
+#' otherwise, use specified.  Default \code{NA}.
+#'
+#' @param chart.with chart width. Default 800.
+#' @param chart.type \emph{pie} or \emph{circle}. Default \emph{pie}.
+#' @param chart.margin chart margin in \emph{list}. Default \code{list(left = 40, right = 20, top = 15, bottom = 25)}.
+#' @param chart.background chart background. Default \emph{transparent}.
+#' @param transition.time chart animation transition time in millisecond.  Default 600.
+#'
+#' @param y.axis.label Y-axis label text. Default \emph{mutations}.
+#' @param axis.label.font css font style shorthand
+#' (\emph{font-style font-variant font-weight font-size/line-height font-family}).
+#' Default \emph{"normal 12px Arial"}.
+#' @param axis.label.color axis label text color. Default \emph{#4f4f4f}.
+#' @param axis.label.alignment axis label text alignment (start/end/middle).  Default \emph{middle}.
+#' @param axis.label.dy text adjustment of axis label text.  Default \emph{-2em}.
+#'
+#' @param legend.margin legend margin in \emph{list}.  Default \code{list(left = 10, right = 0, top = 5, bottom = 5)}.
+#' @param legend.interactive legend interactive mode.  Default \code{TRUE}.
+#' @param legend.title legend title. If \code{NA}, use \emph{factor.col}.  Default is \code{NA}.
+#'
+#' @param lollipop.track.height height of lollipop track. Default 420.
+#' @param lollipop.track.background background of lollipop track.  Default \emph{rgb(244,244,244)}
+#' @param lollipop.pop.min.size lollipop pop minimal size.  Default 2.
+#' @param lollipop.pop.max.size lollipop pop maximal size. Default 12.
+#' @param lollipop.pop.info.limit threshold of lollipop pop size to show count information in middle of pop.  Default 8.
+#' @param lollipop.pop.info.color lollipop pop information text color. Default \emph{#EEE}.
+#' @param lollipop.line.color lollipop line color. Default \emph{rgb(42,42,42)}.
+#' @param lollipop.line.width lollipop line width. Default 0.5.
+#' @param lollipop.circle.color lollipop circle border color. Default \emph{wheat}.
+#' @param lollipop.circle.width lollipop circle border width. Default 0.5.
+#' @param lollipop.label.ratio lollipop click-out label font size to circle size ratio.  Default 1.4.
+#' @param lollipop.label.min.font.size lollipop click-out label minimal font size.  Default 10.
+#' @param lollipop.color.scheme color scheme to fill lollipop pops.  Default \emph{accent}.
+#'
+#' @param title.text title of chart. Default is empty.
+#' @param title.font font of chart title. Default \emph{normal 16px Arial}.
+#' @param title.color color of chart title. Default \emph{#424242}.
+#' @param title.alignment text alignment of chart title (start/middle/end). Default \emph{middle}.
+#' @param title.dy text adjustment of chart title.  Default \emph{0.35em}.
+#'
+#' @param anno.height height of protein structure annotation track.  Default 30.
+#' @param anno.margin margin of protein structure annotation track.  Default \code{list(top = 4, bottom = 0)}.
+#' @param anno.background background of protein structure annotation track.  Default \emph{transparent}.
+#' @param anno.bar.fill background of protein bar in protein structure annotation track.  Default \emph{#e5e3e1}.
+#' @param anno.bar.margin margin of protein bar in protein structure annotation track.  Default \code{list(top = 2, bottom = 2)}.
+#'
+#' @param domain.color.scheme color scheme of protein domains.  Default \emph{category10}.
+#' @param domain.margin margin of protein domains.  Default \code{list(top = 0, bottom = 0)}.
+#' @param domain.text.font domain label text font in shorthand format.  Default \emph{normal 11px Arial}.
+#' @param domain.text.color domain label text color.  Default \emph{#f2f2f2}.
+#'
+#' @param legend if show legend.  Default \code{TRUE}.
+#' @param tooltip if show tooltip.  Default \code{TRUE}.
+#' @param brush if show brush.  Default \code{TRUE}.
+#' @param zoom if enable zoom feature.  Default \code{TRUE}.
+#'
+#' @import htmlwidgets
+#'
+#' @export
+g3Lollipop <- function(mutation.dat,
+                       gene.symbol,
+                       gene.symbol.col = "Hugo_Symbol",
+                       variant.class.col = "Variant_Classification",
+                       protein.change.col = "Protein_Change",
+                       mutation.class.col = "Mutation_Class",
+                       aa.pos.col = "AA_Position",
+                       factor.col = NA,
+                       # chart options
+                       chart.width = 800,
+                       chart.type = "pie",
+                       chart.margin = list(left = 40, right = 20, top = 15, bottom = 25),
+                       chart.background = "transparent",
+                       transition.time = 600,
+                       # axis
+                       y.axis.label = "mutations",
+                       axis.label.font = "normal 12px Arial",
+                       axis.label.color = "#4f4f4f",
+                       axis.label.alignment = "middle",
+                       axis.label.dy = "-2em",
+                       # legend
+                       legend.margin = list(left = 10, right = 0, top = 5, bottom = 5),
+                       legend.interactive = TRUE,
+                       legend.title = NA,
+                       # lollipop track
+                       lollipop.track.height = 420,
+                       lollipop.track.background = "rgb(244,244,244)",
+                       # pop size
+                       lollipop.pop.min.size = 2,
+                       lollipop.pop.max.size = 12,
+                       lollipop.pop.info.limit = 8,
+                       lollipop.pop.info.color = "#EEE",
+                       lollipop.line.color = "rgb(42,42,42)",
+                       lollipop.line.width = 0.5,
+                       lollipop.circle.color = "wheat",
+                       lollipop.circle.width = 0.5,
+                       lollipop.label.ratio = 1.4,
+                       lollipop.label.min.font.size = 10,
+                       lollipop.color.scheme = "accent",
+                       # title text
+                       title.text = "",
+                       title.font = "normal 16px Arial",
+                       title.color = "#424242",
+                       title.alignment = "middle",
+                       title.dy = "0.35em",
+                       # annotation track
+                       anno.height = 30,
+                       anno.margin = list(top = 4, bottom = 0),
+                       anno.background = "transparent",
+                       anno.bar.fill = "#e5e3e1",
+                       anno.bar.margin = list(top = 2, bottom = 2),
+                       # domain
+                       domain.color.scheme = "category10",
+                       domain.margin = list(top = 0, bottom = 0),
+                       domain.text.font = "normal 11px Arial",
+                       domain.text.color = "#f2f2f2",
+                       # others
+                       legend = TRUE,
+                       tooltip = TRUE,
+                       brush = TRUE,
+                       zoom = TRUE
+                       ){
+  # check gene.symbol
+  if(is.null(gene.symbol)){
+    stop("Please provide a gene symbol")
+  }
+
+  # check if all required columns exists in mut.dat
+  mut.required.col <- c(gene.symbol.col, variant.class.col, protein.change.col)
+
+  missing.columns <- mut.required.col[!mut.required.col %in% colnames(mutation.dat)]
+  if(length(missing.columns) > 0){
+    message(mutation.dat, " contains columns: ", paste(colnames(mutation.dat), collapse = ", "))
+    stop("Some columns are missing in mutation data: ", paste(missing.columns, collapse = ", "))
+  }
+
+  # if need to check "mutation.class.col" or "aa.pos.col"
+  # parse Mutation_Class
+  if(!mutation.class.col %in% colnames(mutation.dat)){
+    mutation.dat[, mutation.class.col] <- mapMutationTypeToMutationClass(mutation.dat[, variant.class.col])
+  }
+
+  # parse amino-acid position
+  if(!aa.pos.col %in% colnames(mutation.dat)){
+    mutation.dat[, aa.pos.col] <- parseProteinChange(mutation.dat[, protein.change.col],
+                                                     mutation.dat[, mutation.class.col])
+  }
+
+  # check if by.factor column exists
+  if(is.na(factor.col)){
+    factor.col <- mutation.class.col
+  }
+  if(!factor.col %in% colnames(mutation.dat)){
+    stop("No ", factor.col, " column in ", maf.file)
+  }
+
+  if(is.na(legend.title)){
+    legend.title <- factor.col
+  }
+
+  # get mutation data for the given gene
+  snv.data.df <- mutation.dat[mutation.dat[, gene.symbol.col] == gene.symbol
+                              & !is.na(mutation.dat[, aa.pos.col]), ]
+  snv.data.json <- jsonlite::toJSON(snv.data.df, pretty = FALSE, auto_unbox = TRUE)
+
+  # get protein domain information
+  domain.data.json <- hgnc2pfam(gene.symbol)
+
+  # read in data
+  snv.data.format <- list(
+    x = aa.pos.col,
+    y = protein.change.col,
+    factor = factor.col
+  )
+
+  snv.data.format.json <- jsonlite::toJSON(snv.data.format, pretty = FALSE, auto_unbox = TRUE)
+
+  # domain data format
+  domain.data.format = list(
+    length = "length",
+    domainType = "pfam",
+    details = list(
+      start = "start",
+      end = "end",
+      name = "hmm.name"
+    )
+  )
+  domain.data.format.json = jsonlite::toJSON(domain.data.format, pretty = FALSE, auto_unbox = TRUE)
+
+  # plot settings
+  plot.settings <- list(
+    chartWidth = chart.width,
+    chartType = chart.type,
+    chartMargin = chart.margin,
+    chartBackground = chart.background,
+    transitionTime = transition.time,
+    # axis
+    yAxisLabel = y.axis.label,
+    axisLabelFont = axis.label.font,
+    axisLabelColor = axis.label.color,
+    axisLabelAlignment = axis.label.alignment,
+    axisLabelDy = axis.label.dy,
+    # legend
+    legendMargin = legend.margin,
+    legendInteractive = legend.interactive,
+    legendTitle = legend.title,
+    # lollipop track
+    lollipopTrackHeight = lollipop.track.height,
+    lollipopTrackBackground = lollipop.track.background,
+    # pop size
+    lollipopPopMinSize = lollipop.pop.min.size,
+    lollipopPopMaxSize = lollipop.pop.max.size,
+    lollipopPopInfoLimit = lollipop.pop.info.limit,
+    lollipopPopInfoColor = lollipop.pop.info.color,
+    lollipopLineColor = lollipop.line.color,
+    lollipopLineWidth = lollipop.line.width,
+    lollipopCircleColor = lollipop.circle.color,
+    lollipopCircleWidth = lollipop.circle.width,
+    lollipopLabelRatio = lollipop.label.ratio,
+    lollipopLabelMinFontSize = lollipop.label.min.font.size,
+    lollipopColorScheme = lollipop.color.scheme,
+    # title text
+    titleText = title.text,
+    titleFont = title.font,
+    titleColor = title.color,
+    titleAlignment = title.alignment,
+    titleDy = title.dy,
+    # annotation track
+    annoHeight = anno.height,
+    annoMargin = anno.margin,
+    annoBackground = anno.background,
+    annoBarFill = anno.bar.fill,
+    annoBarMargin = anno.bar.margin,
+    # domain
+    domainColorScheme = domain.color.scheme,
+    domainMargin = domain.margin,
+    domainTextFont = domain.text.font,
+    domainTextColor = domain.text.color,
+    # others
+    legend = legend,
+    tooltip = tooltip,
+    brush = brush,
+    zoom = zoom
+  )
+
+  plot.settings.json <- jsonlite::toJSON(plot.settings, pretty = FALSE, auto_unbox = TRUE)
+
+  x <- list(
+    domainData = domain.data.json,
+    domainDataFormat = domain.data.format.json,
+    snvData = snv.data.json,
+    snvDataFormat = snv.data.format.json,
+    plotSettings = plot.settings.json
+  )
+
+  htmlwidgets::createWidget(
+    name = "g3Lollipop",
+    x,
+    package = "g3viz"
+  )
+
+#  plot.settings.json
+}
+
+#' Shiny bindings for g3-lollipop
+#'
+#' Output and render functions for using g3-lollipop within Shiny
+#' applications and interactive Rmd documents.
+#'
+#' @param outputId output variable to read from
+#' @param width,height Must be a valid CSS unit (like \code{'100\%'},
+#'   \code{'400px'}, \code{'auto'}) or a number, which will be coerced to a
+#'   string and have \code{'px'} appended.
+#' @param expr An expression that generates a g3-lollipop
+#' @param env The environment in which to evaluate \code{expr}.
+#' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
+#'   is useful if you want to save an expression in a variable.
+#'
+#' @name g3-lollipop-shiny
+#'
+#' @export
+g3LollipopOutput <- function(outputId, width = '100%', height = '400px'){
+  htmlwidgets::shinyWidgetOutput(outputId, 'g3-lollipop', width, height, package = 'g3viz')
+}
+
+#' @rdname g3-lollipop-shiny
+#' @export
+renderG3Lollipop <- function(expr, env = parent.frame(), quoted = FALSE) {
+  if (!quoted) { expr <- substitute(expr) } # force quoted
+  htmlwidgets::shinyRenderWidget(expr, g3-lollipopOutput, env, quoted = TRUE)
+}