G3viz: chart themes"
In g3viz: Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram

# install package
library(g3viz)
library(cBioPortalData)
library(knitr)

knitr::opts_chunk$set(
    echo = TRUE,
    collapse = TRUE,
    comment = "#>"
)

The g3viz package contains 8 ready-to-use chart schemes: default, blue, simple, cbioportal, nature, nature2, ggplot2, and dark.

# read data
mutation.dat <- readMAF("tables/tp53-msk_impact_2017.tsv", sep="\t")

default theme

chart.options = g3Lollipop.theme(
      theme.name = "default",
      title.text = "default theme title",
      y.axis.label = "y-label",
      legend.title = "legend-title")

g3Lollipop(mutation.dat,
           plot.options = chart.options,
           btn.style = "blue",
           gene.symbol = "TP53")

blue theme

g3Lollipop(mutation.dat,
           plot.options =
             g3Lollipop.theme(theme.name = "blue",
                              title.text = "blue theme title",
                              y.axis.label = "y-label",
                              legend.title = "legend-title"),
           btn.style = "blue",
           gene.symbol = "TP53")

simple theme

g3Lollipop(mutation.dat,
           plot.options =
             g3Lollipop.theme(theme.name = "simple",
                              title.text = "simple theme title",
                              y.axis.label = "y-label",
                              legend.title = "legend-title"),
           btn.style = "blue",
           gene.symbol = "TP53")

cbioportal theme

g3Lollipop(mutation.dat,
           plot.options =
             g3Lollipop.theme(theme.name = "cbioportal",
                              title.text = "cbioportal theme title",
                              y.axis.label = "y-label",
                              legend.title = "legend-title"),
           btn.style = "blue",
           gene.symbol = "TP53")

nature theme

g3Lollipop(mutation.dat,
           plot.options =
             g3Lollipop.theme(theme.name = "nature",
                              title.text = "nature theme title",
                              y.axis.label = "y-label",
                              legend.title = "legend-title"),
           btn.style = "blue",
           gene.symbol = "TP53")

nature2 theme

g3Lollipop(mutation.dat,
           plot.options =
             g3Lollipop.theme(theme.name = "nature2",
                              title.text = "nature2 theme title",
                              y.axis.label = "y-label",
                              legend.title = "legend-title"),
           btn.style = "blue",
           gene.symbol = "TP53")

ggplot2 theme

g3Lollipop(mutation.dat,
           plot.options =
             g3Lollipop.theme(theme.name = "ggplot2",
                              title.text = "ggplot2 theme title",
                              y.axis.label = "y-label",
                              legend.title = "legend-title"),
           btn.style = "blue",
           gene.symbol = "TP53")

dark theme

g3Lollipop(mutation.dat,
           plot.options =
             g3Lollipop.theme(theme.name = "dark",
                              title.text = "dark theme title",
                              y.axis.label = "y-label",
                              legend.title = "legend-title"),
           btn.style = "blue",
           gene.symbol = "TP53")