基因突变棒棒糖图，让你的突变作图美起来！

install.packages("g3viz", repos = "http://cran.us.r-project.org")

#检查R包devtools是否安装
if("devtools" %in% rownames(installed.packages()) == FALSE){
  install.packages("devtools")
}

# install from github
devtools::install_github("g3viz/g3viz")

#注意此时字母均为小写
library("g3viz")

# System file
maf.file <- system.file("extdata", "TCGA.BRCA.varscan.somatic.maf.gz", package = "g3viz")

mutation.dat <- readMAF(maf.file)chart.options <- g3Lollipop.theme(theme.name = "default",
                                  title.text = "PIK3CA gene (default theme)")

g3Lollipop(mutation.dat,
           gene.symbol = "PIK3CA",
           plot.options = chart.options,
           output.filename = "default_theme")

Hugo_Symbol,Chromosome,Start_Position,End_Position,Strand,Variant_Classification,Variant_Type,Reference_Allele,Tumor_Seq_Allele1,Tumor_Seq_Allele2,amino_acid_change

# load data
mutation.csv <- system.file("extdata", "ccle.csv", package = "g3viz")
mutation.dat <- readMAF(mutation.csv,
                        gene.symbol.col = "Hugo_Symbol",
                        variant.class.col = "Variant_Classification",
                        protein.change.col = "amino_acid_change",
                        sep = ",")  # column-separator of csv file
g3Lollipop(mutation.dat,
           gene.symbol = "TP53",
           protein.change.col = "amino_acid_change",
           btn.style = "blue", # blue-style chart download buttons
           output.filename = "customized_plot")

# Retrieve mutation data of "msk_impact_2017" from cBioPortal
mutation.dat <- getMutationsFromCbioportal("msk_impact_2017", "TP53")

# "cbioportal" chart theme
plot.options <- g3Lollipop.theme(theme.name = "cbioportal",
                                 title.text = "TP53 gene (cbioportal theme)",
                                 y.axis.label = "# of TP53 Mutations")

g3Lollipop(mutation.dat,
           gene.symbol = "TP53",
           btn.style = "gray", # gray-style chart download buttons
           plot.options = plot.options,
           output.filename = "cbioportal_theme")

install_github("cBioPortal/cgdsr")

library(cgdsr)
cgds <- CGDS("http://www.cbioportal.org/")
# To list all studies
all.studies <- cgdsr::getCancerStudies(cgds)
# Pick up a cancer study with mutation data
mutation.dat <- g3viz::getMutationsFromCbioportal("all_stjude_2016", "TP53")

# set up chart options
plot.options <- g3Lollipop.options(
  # Chart settings
  chart.width = 600,
  chart.type = "pie",
  chart.margin = list(left = 30, right = 20, top = 20, bottom = 30),
  chart.background = "#d3d3d3",
  transition.time = 300,
  # Lollipop track settings
  lollipop.track.height = 200,
  lollipop.track.background = "#d3d3d3",
  lollipop.pop.min.size = 1,
  lollipop.pop.max.size = 8,
  lollipop.pop.info.limit = 5.5,
  lollipop.pop.info.dy = "0.24em",
  lollipop.pop.info.color = "white",
  lollipop.line.color = "#a9A9A9",
  lollipop.line.width = 3,
  lollipop.circle.color = "#ffdead",
  lollipop.circle.width = 0.4,
  lollipop.label.ratio = 2,
  lollipop.label.min.font.size = 12,
  lollipop.color.scheme = "dark2",
  highlight.text.angle = 60,
  # Domain annotation track settings
  anno.height = 16,
  anno.margin = list(top = 0, bottom = 0),
  anno.background = "#d3d3d3",
  anno.bar.fill = "#a9a9a9",
  anno.bar.margin = list(top = 4, bottom = 4),
  domain.color.scheme = "pie5",
  domain.margin = list(top = 2, bottom = 2),
  domain.text.color = "white",
  domain.text.font = "italic 8px Serif",
  # Y-axis label
  y.axis.label = "# of TP53 gene mutations",
  axis.label.color = "#303030",
  axis.label.alignment = "end",
  axis.label.font = "italic 12px Serif",
  axis.label.dy = "-1.5em",
  y.axis.line.color = "#303030",
  y.axis.line.width = 0.5,
  y.axis.line.style = "line",
  y.max.range.ratio = 1.1,
  # Chart title settings
  title.color = "#303030",
  title.text = "TP53 gene (customized chart options)",
  title.font = "bold 12px monospace",
  title.alignment = "start",
  # Chart legend settings
  legend = TRUE,
  legend.margin = list(left=20, right = 0, top = 10, bottom = 5),
  legend.interactive = TRUE,
  legend.title = "Variant classification",
  # Brush selection tool
  brush = TRUE,
  brush.selection.background = "#F8F8FF",
  brush.selection.opacity = 0.3,
  brush.border.color = "#a9a9a9",
  brush.border.width = 1,
  brush.handler.color = "#303030",
  # tooltip and zoom
  tooltip = TRUE,
  zoom = TRUE
)

OptionDescription
Chart settings    
chart.width    chart width in px. Default 800.    
chart.type    pop type, pie or circle. Default pie.    
chart.margin    specify chart margin in list format. Default list(left = 40, right = 20, top = 15, bottom = 25).    
chart.background    chart background. Default transparent.    
transition.time    chart animation transition time in millisecond. Default 600.    
Lollipop track settings    
lollipop.track.height    height of lollipop track. Default 420.    
lollipop.track.background    background of lollipop track. Default rgb(244,244,244).    
lollipop.pop.min.size    lollipop pop minimal size in px. Default 2.    
lollipop.pop.max.size    lollipop pop maximal size in px. Default 12.    
lollipop.pop.info.limit    threshold of lollipop pop size to show count information in middle of pop. Default 8.    
lollipop.pop.info.color    lollipop pop information text color. Default #EEE.    
lollipop.pop.info.dy    y-axis direction text adjustment of lollipop pop information. Default -0.35em.    
lollipop.line.color    lollipop line color. Default rgb(42,42,42).    
lollipop.line.width    lollipop line width. Default 0.5.    
lollipop.circle.color    lollipop circle border color. Default wheat.    
lollipop.circle.width    lollipop circle border width. Default 0.5.    
lollipop.label.ratio    lollipop click-out label font size to circle size ratio. Default 1.4.    
lollipop.label.min.font.size    lollipop click-out label minimal font size. Default 10.    
lollipop.color.scheme    color scheme to fill lollipop pops. Default accent. Check color schemes for details.    
highlight.text.angle    the rotation angle of on-click highlight text in degree. Default 90.    
Domain annotation track settings    
anno.height    height of protein structure annotation track. Default 30.    
anno.margin    margin of protein structure annotation track. Default list(top = 4, bottom = 0).    
anno.background    background of protein structure annotation track. Default transparent.    
anno.bar.fill    background of protein bar in protein structure annotation track. Default #E5E3E1.    
anno.bar.margin    margin of protein bar in protein structure annotation track. Default list(top = 2, bottom = 2).    
domain.color.scheme    color scheme of protein domains. Default category10. Check color schemes for details.    
domain.margin    margin of protein domains. Default list(top = 0, bottom = 0).    
domain.text.font    domain label text font in shorthand format. Default normal 11px Arial.    
domain.text.color    domain label text color. Default #F2F2F2.    
Y-axis settings    
y.axis.label    Y-axis label text. Default # of mutations.    
axis.label.font    css font style shorthand (font-style font-variant font-weight font-size/line-height font-family). Default normal 12px Arial.    
axis.label.color    axis label text color. Default #4f4f4f.    
axis.label.alignment    axis label text alignment (start/end/middle). Default middle    
axis.label.dy    text adjustment of axis label text. Default -2em.    
y.axis.line.color    color of y-axis in-chart lines (ticks). Default #c4c8ca.    
y.axis.line.style    style of y-axis in-chart lines (ticks), dash or line. Default dash.    
y.axis.line.width    width of y-axis in-chart lines (ticks). Default 1.    
y.max.range.ratio    ratio of y-axis range to data value range. Default 1.1.    
Chart title settings    
title.text    title of chart. Default "".    
title.font    font of chart title. Default normal 16px Arial.    
title.color    color of chart title. Default #424242.    
title.alignment    text alignment of chart title (start/middle/end). Default middle.    
title.dy    text adjustment of chart title. Default 0.35em.    
Chart legend settings    
legend    if show legend. Default TRUE.    
legend.margin    legend margin in list format. Default list(left = 10, right = 0, top = 5, bottom = 5).    
legend.interactive    legend interactive mode. Default TRUE.    
legend.title    legend title. If NA, use factor name as factor.col. Default is NA.    
Brush selection tool settings    
brush    if show brush. Default TRUE.    
brush.selection.background    background color of selection brush. Default #666.    
brush.selection.opacity    background opacity of selection brush. Default 0.2.    
brush.border.color    border color of selection brush. Default #969696.    
brush.handler.color    color of left and right handlers of selection brush. Default #333.    
brush.border.width    border width of selection brush. Default 1.    
Tooltip and zoom tools    
tooltip    if show tooltip. Default TRUE.    
zoom    if enable zoom feature. Default TRUE.