Package 'g3viz'

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")

---

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

outputId	output variable to read from
width, height	Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.
expr	An expression that generates a g3-lollipop
env	The environment in which to evaluate expr.
quoted	Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

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

chart.width	chart width. Default 800.
chart.type	pie or circle. Default circle.
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	animation transition time when clicking lollipop pops to show labels (in millisecond). Default 600.
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.
legend.margin	legend margin in list. Default list(left = 10, right = 0, top = 5, bottom = 5).
legend.interactive	legend interactive mode. Default TRUE.
legend.title	legend title. If NA, factor.col in g3Lollipop is used. Default is NA.
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. Default 2.
lollipop.pop.max.size	lollipop pop maximal size. 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.
highlight.text.angle	pop-on-click highlight text angle. Default 90.
title.text	title of chart. Default is empty.
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.
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.
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.
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.
legend	if show legend. Default TRUE.
tooltip	if show tooltip. Default TRUE.
zoom	if enable zoom feature. Default TRUE.

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

theme.name	theme name, including default, cbioportal, nature, nature2, dark, blue, ggplot2, and simple. Default default.
title.text	title of chart. Default is empty.
y.axis.label	Y-axis label text. Default "# of mutations".
legend.title	legend title. If NA, factor.col in g3Lollipop is used. Default is NA.

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

study.id	cbioprotal study ID
gene.symbol	HGNC gene symbol.
output.file	if specified, output to a file in CSV format. Default is NA.
mutation.type.to.class.df	mapping table from mutation type to class. See mapMutationTypeToMutationClass for details. Default NA, which indicates to use default mappings.

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

maf.df	MAF data frame
alt.column.names	a vector of alternative column names

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

hgnc.symbol	primary Hugo symbol
guess	if the given Hugo symbol links to multiple UniProt IDs, choose the longest one (guess == TRUE); otherwise NA (guess == FALSE). Default TRUE.
uniprot.id	UniProt ID, in case that gene symbol maps to multiple UniProt entries.
output.format	output format: JSON or list

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

hgnc.symbol

primary HUGO symbol

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

mutation.type.vec	a vector of mutation type information
mutation.type.to.class.df	A mapping table from mutation type (header Mutation_Type) to mutation class (header Mutation_Class). Default NA, which indicates to use default mappings.

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

protein.change.vec	a vector of strings with protein change information, usually in HGVSp_short format.
mutation.class.vec	a vector of strings with mutation class (or so-called variant classification) information.

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

maf.file	MAF file name. Gnuzipped input file allowed, with ".gz" file extension.
gene.symbol.col	Column name of Hugo gene symbols (e.g., TP53). Default Hugo_Symbol.
variant.class.col	Column name for variant class information (e.g., Missense_Mutation, Nonsense_Mutation). Default is the first match of Variant_Classification or Mutation_Type.
protein.change.col	Column name for protein change information (e.g., p.K960R, G658S, L14Sfs*15). Default is the first match of Protein_Change or HGVSp_Short.
if.parse.aa.pos	if parse amino-acid position of mutations. Default is TRUE.
if.parse.mutation.class	if parse mutation class from mutation type (variant classification) information. Default is TRUE.
mutation.class.col	Column name of the parsed mutation class. Default Mutation_Class.
aa.pos.col	Column name of the parsed amino-acid change position. Default AA_Position.
mutation.type.to.class.df	mapping table from mutation type to class. mapMutationTypeToMutationClass for details. Default NA, which indicates to use default mappoings.
sep	separator of columns. Default sep = "\t".
quote	the set of quoting characters. To disable quoting altogether, use quote = "". Default quote = "".
...	additional parameters pass to read.table.

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

uniprot.id

UniProt ID

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")

---