g3viz (version 1.2.0)

g3Lollipop: 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"
)

Value

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

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.

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")