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

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")

Shiny bindings for g3Lollipop

Description

Output and render functions for using g3viz lollipop diagram within Shiny applications and interactive Rmd documents.

Usage

g3LollipopOutput(outputId, width = "100%", height = "520px")

renderG3Lollipop(expr, env = parent.frame(), quoted = FALSE)

Arguments

Value

No value returned. It is the binding which enables interactive functions within Shiny applications and Rmd documents.

G3Lollipop plot options

Description

G3Lollipop plot options

Usage

g3Lollipop.options(
  chart.width = 800,
  chart.type = "circle",
  chart.margin = list(left = 40, right = 20, top = 15, bottom = 25),
  chart.background = "transparent",
  transition.time = 600,
  y.axis.label = "# of mutations",
  axis.label.font = "normal 12px Arial",
  axis.label.color = "#4f4f4f",
  axis.label.alignment = "middle",
  axis.label.dy = "-2em",
  y.axis.line.color = "#c4c8ca",
  y.axis.line.style = "dash",
  y.axis.line.width = 1,
  y.max.range.ratio = 1.1,
  legend.margin = list(left = 10, right = 0, top = 5, bottom = 5),
  legend.interactive = TRUE,
  legend.title = NA,
  lollipop.track.height = 420,
  lollipop.track.background = "rgb(233,233,233)",
  lollipop.pop.min.size = 2,
  lollipop.pop.max.size = 12,
  lollipop.pop.info.limit = 8,
  lollipop.pop.info.color = "#EEE",
  lollipop.pop.info.dy = "0.35em",
  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",
  highlight.text.angle = "90",
  title.text = "",
  title.font = "normal 16px Arial",
  title.color = "#424242",
  title.alignment = "middle",
  title.dy = "0.35em",
  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.color.scheme = "category10",
  domain.margin = list(top = 0, bottom = 0),
  domain.text.font = "normal 11px Arial",
  domain.text.color = "#f2f2f2",
  brush = TRUE,
  brush.selection.background = "#666",
  brush.selection.opacity = 0.2,
  brush.border.color = "#969696",
  brush.handler.color = "#333",
  brush.border.width = 1,
  legend = TRUE,
  tooltip = TRUE,
  zoom = TRUE
)

Arguments

Value

a list with g3Lollipop plot options

G3Lollipop chart options of built-in themes.

Description

G3Lollipop chart options of built-in themes.

Usage

g3Lollipop.theme(
  theme.name = "default",
  title.text = "",
  y.axis.label = "# of mutations",
  legend.title = NA
)

Arguments

Value

a list with g3Lollipop plot options

Query cancer genomic mutation data from cBioPortal

Description

Retrieve and parse mutation data from cBioPortal by the given cBioPortal cancer study ID and the gene symbol.

Usage

getMutationsFromCbioportal(
  study.id,
  gene.symbol,
  output.file = NA,
  mutation.type.to.class.df = NA
)

Arguments

Value

a data frame with columns

Hugo_Symbol

Hugo gene symbol

Protein_Change

Protein change information (cBioportal uses HGVSp format)

Sample_ID

Sample ID

Mutation_Type

mutation type, aka, variant classification.

Chromosome

chromosome

Start_Position

start position

End_Position

end position

Reference_Allele

reference allele

Variant_Allele

variant allele

Mutation_Class

mutation class (e.g., Truncating/Missense/Inframe/Other)

AA_Position

amino-acid position of the variant; if the variant is not in protein-coding region, NA

Examples

# Usage:

Guess column name for MAF file

Description

Guess column name for MAF file

Usage

guessMAFColumnName(maf.df, alt.column.names)

Arguments

Value

if hit one alternative column name, return the name; otherwise, return NA

Map from Hugo symbol to Pfam domains

Description

Mapping from Hugo symbol to Pfam-A domain composition. If the given Hugo symbol has multiple UniProt ID mappings, and guess == TRUE, the longest UniProt protein is selected. Return is either a list of a JSON.

Usage

hgnc2pfam(hgnc.symbol, guess = TRUE, uniprot.id = NA, output.format = "json")

Arguments

Value

A list or a JSON with attributes: symbol, uniprot, length, and a list of Pfam entries, including hmm.acc, hmm.name, start, end, and type.

Examples

# general usage
hgnc2pfam("TP53")
hgnc2pfam("TP53", output.format = "json")
hgnc2pfam("TP53", output.format = "list")
hgnc2pfam("TP53", output.format = "json", uniprot.id = "P04637") # OK

# for gene mapping to multiple UniProt enties
hgnc2pfam("GNAS", guess = TRUE)
hgnc2pfam("GNAS", guess = FALSE)
hgnc2pfam("GNAS", output.format = "list")
hgnc2pfam("GNAS", output.format = "list", uniprot.id = "P84996")
## Not run: 
hgnc2pfam("GNAS", output.format = "list", uniprot.id = "P84997") # , returns FALSE

## End(Not run)

hgnc2pfam("PRAMEF9", output.format = "list") # no Pfam mappings

Mapping table between gene.symbol, uniprot.id, and pfam

Description

A dataset containing the mapping table between Hugo symbol, UniProt ID, and Pfam ACC.

Usage

hgnc2pfam.df

Format

A data frame with columns:

symbol

Gene symbol

uniprot

UniProt ID

length

protein length

start

starting position of Pfam domain

end

ending position of Pfam domain

hmm.acc

Pfam accession number

hmm.name

Pfam name

type

Pfam type, i.e., domain/family/motif/repeat/disordered/coiled-coil

Source

Pfam (v31.0) and UniProt

Examples

hgnc2pfam.df

Mapping from Hugo symbol to UniProt IDs

Description

Mapping from Hugo Symbol to UniProt ID using internal mapping table. Return a data frame with columns symbol (Hugo symbol), uniprot (UniProt ID), and length (protein length).

Usage

hgnc2uniprot(hgnc.symbol)

Arguments

Value

a data frame with columns symbol (Hugo symbol), uniprot (UniProt ID), and length (protein length).

Examples

# maps to single UniProt entry
hgnc2uniprot("TP53")

# maps to multiple UniProt entries
hgnc2uniprot("GNAS")
hgnc2uniprot("AKAP7")

Map from mutation type (aka, variant classification) to mutation class

Description

Map from mutation type (aka, variant classification) to mutation class. Default mappings are as follows,

• Missense

  • Missense_Mutation — a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid See https://en.wikipedia.org/wiki/Missense_mutation.

• Inframe

  • In_Frame_Del — a deletion that keeps the sequence in frame

  • In_Frame_Ins — an insertion that keeps the sequence in frame

  • Silent — variant is in coding region of the chosen transcript, but protein structure is identical (i.e., a synonymous mutation)

  • Targeted_Region — targeted region

• Truncating

  • Frame_Shift — a variant caused by indels of a number of nucleotides in a DNA sequence that is not divisible by three. See https://en.wikipedia.org/wiki/Frameshift_mutation.

  • Frame_Shift_Ins — a variant caused by insertion that moves the coding sequence out of frame. See https://en.wikipedia.org/wiki/Frameshift_mutation.

  • Frame_Shift_Del — a variant caused by deletion that moves the coding sequence out of frame. See https://en.wikipedia.org/wiki/Frameshift_mutation.

  • Nonsense_Mutation — a premature stop codon that is created by the variant. See https://en.wikipedia.org/wiki/Nonsense_mutation.

  • Nonstop_Mutation — a variant that removes stop codon.

  • Splice_Site — a variant that is within two bases of a splice site.

  • Splice_Region — a variant that is within splice region.

• Other

  • 5'UTR — a variant that is on the 5'UTR for the chosen transcript.

  • 3'UTR — a variant that is on the 3'UTR for the chosen transcript.

  • 5'Flank — a variant that is upstream of the chosen transcript (generally within 3kb).

  • 3'Flank — a variant that is downstream of the chosen transcript (generally within 3kb).

  • Fusion — a gene fusion.

  • IGR — an intergenic region. Does not overlap any transcript.

  • Intron — a variant that lies between exons within the bounds of the chosen transcript.

  • Translation_Start_Site — a variant that is in translation start site.

  • De_novo_Start_InFrame — a novel start codon that is created by the given variant using the chosen transcript. However, it is in frame relative to the coded protein.

  • De_novo_Start_OutOfFrame — a novel start codon that is created by the given variant using the chosen transcript. However, it is out of frame relative to the coded protein.

  • Start_Codon_SNP — a point mutation that overlaps the start codon.

  • Start_Codon_Ins — an insertion that overlaps the start codon.

  • Start_Codon_Del — a deletion that overlaps the start codon.

  • RNA — a variant that lies on one of the RNA transcripts.

  • lincRNA — a variant that lies on one of the lincRNAs.

  • Unknown — Unknown

Usage

mapMutationTypeToMutationClass(
  mutation.type.vec,
  mutation.type.to.class.df = NA
)

Arguments

Value

a vector of mapped mutation class information

Default mapping table between mutation type (aka, variant classification) to mutation class

Description

A dataset containing the mapping table between genomic mutation type (aka, variant classification) to mutation class. See mapMutationTypeToMutationClass for details.

Usage

mutation.table.df

Format

A data frame with three columns:

Mutation_Type

Mutation type, aka, variant classification

Mutation_Class

mutation class

Short_Name

short name of mutation type

Examples

mutation.table.df

Extract amino_acid_position from Protein_Change

Description

Parse amino_acid_position according to HGVSp_short format.
For example, p.Q16Rfs*28, amino-acid position is 16. See http://varnomen.hgvs.org/recommendations/protein/ or https://www.hgvs.org/mutnomen/recs-prot.html.

Usage

parseProteinChange(protein.change.vec, mutation.class.vec)

Arguments

Value

a vector of parsed amino-acid position

Read MAF file

Description

Read mutation information from MAF file. For MAF format specification, see https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/.

Usage

readMAF(
  maf.file,
  gene.symbol.col = "Hugo_Symbol",
  variant.class.col = c("Variant_Classification", "Mutation_Type"),
  protein.change.col = c("Protein_Change", "HGVSp_Short"),
  if.parse.aa.pos = TRUE,
  if.parse.mutation.class = TRUE,
  mutation.class.col = "Mutation_Class",
  aa.pos.col = "AA_Position",
  mutation.type.to.class.df = NA,
  sep = "\t",
  quote = "",
  ...
)

Arguments

Value

a data frame containing MAF information, plus optional columns of the parsed Mutation_Class and Protein_Position.

From UniProt ID to Pfam-A domain composition

Description

Map from UniProt ID to Pfam-A domain composition.

Usage

uniprot2pfam(uniprot.id)

Arguments

Value

a data frame with columns

• uniprot — UniProt ID

• length — protein length

• hmm.acc — accession number of Pfam HMM model, e.g., PF08563

• hmm.name — Pfam name, e.g., P53_TAD

• start — Pfam domain start position

• end — Pfam domain end position

• type — Pfam type, including domain/motif/family

Examples

uniprot2pfam("Q5VWM5")  # PRAMEF9; PRAMEF15
uniprot2pfam("P04637")