g3Lollipop: Render g3lollipop diagram for the given mutation data

In g3viz: Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram

Render g3lollipop diagram for the given mutation data

Description

Render g3lollipop diagram for the given mutation data

Usage

g3Lollipop(
  mutation.dat,
  gene.symbol,
  uniprot.id = NA,
  gene.symbol.col = "Hugo_Symbol",
  aa.pos.col = "AA_Position",
  protein.change.col = c("Protein_Change", "HGVSp_Short"),
  factor.col = "Mutation_Class",
  plot.options = g3Lollipop.options(),
  save.png.btn = TRUE,
  save.svg.btn = TRUE,
  btn.style = NA,
  output.filename = "output"
)

Arguments

mutation.dat	Input genomic mutation data frame
gene.symbol	HGNC primary gene symbol
uniprot.id	UniProt ID, in case that the specified gene symbol links to multiple UniProt entries (isoforms). For example, AKAP7 gene has two isoforms in UniProt, O43687 and Q9P0M2.
gene.symbol.col	Column name of Hugo gene symbols (e.g., TP53). Default Hugo_Symbol.
aa.pos.col	Column name of the parsed amino-acid change position. Default AA_Position.
protein.change.col	Column name of protein change information (e.g., p.K960R, G658S, L14Sfs*15). Default is a list of Protein_Change, HGVSp_Short.
factor.col	column of classes in the plot legend. IF NA, use parsed Mutation_Class column, otherwise, use specified. Default NA.
plot.options	g3lollipop diagram options in list format. Check g3Lollipop.options
save.png.btn	If add save-as-png button to the diagram. Default TRUE.
save.svg.btn	If add save-as-svg button to the diagram. Default TRUE.
btn.style	button style, including browser default button style, and two built-in styles, blue or gray. Default NA, indicating browser default.
output.filename	Specify output file name.

Value

lollipop diagram for the given mutation data. The chart is interactive within either Shiny applications or Rmd documents under the bindings.

Examples

# system mutation data
maf.file <- system.file("extdata", "TCGA.BRCA.varscan.somatic.maf.gz", package = "g3viz")
# read in MAF file
mutation.dat <- readMAF(maf.file)

# use built-in chart theme
chart.options <- g3Lollipop.theme(theme.name = "default",
                                  title.text = "PIK3CA gene (default theme)")
# generate chart
g3Lollipop(mutation.dat,
           gene.symbol = "PIK3CA",
           plot.options = chart.options,
           btn.style = "blue",
           output.filename = "default_theme")

g3viz documentation built on Aug. 19, 2022, 5:07 p.m.