G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram

1 Introduction

Intuitively and effectively visualizing genetic mutation data can help researchers to better understand genomic data and validate findings. G3viz is an R package which provides an easy-to-use lollipop-diagram tool. It enables users to interactively visualize detailed translational effect of genetic mutations in RStudio or a web browser, without having to know any HTML5/JavaScript technologies.

The features of g3viz include

• Interactive (zoom & pan, tooltip, brush selection tool, and interactive legend)
• Highlight and label positional mutations
• 8 ready-to-use chart themes
• Highly customizable with over 50 chart options and over 35 color schemes
• Save charts in PNG or high-quality SVG format
• Built-in function to retrieve protein domain information and resolve gene isoforms
• Built-in function to map genetic mutation type (a.k.a, variant classification) to mutation class

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2 Install g3viz

Install from R repository

# install package
install.packages("g3viz", repos = "http://cran.us.r-project.org")

or install development version from github

# Check if "devtools" installed
if("devtools" %in% rownames(installed.packages()) == FALSE){ 
  install.packages("devtools")
}

# install from github
devtools::install_github("g3viz/g3viz")

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3 Quick Start

# load g3viz package
library(g3viz)

3.1 Example 1: Visualize genetic mutation data from MAF file

Mutation Annotation Format (MAF) is a commonly-used tab-delimited text file for storing aggregated mutation information. It could be generated from VCF file using tools like vcf2maf. Translational effect of variant alleles in MAF files are usually in the column named Variant_Classification or Mutation_Type (i.e., Frame_Shift_Del, Split_Site). In this example, the somatic mutation data of the TCGA-BRCA study was originally downloaded from the GDC Data Portal.

# System file
maf.file <- system.file("extdata", "TCGA.BRCA.varscan.somatic.maf.gz", package = "g3viz")

# ============================================
# Read in MAF file
#   In addition to read data in, g3viz::readMAF function does
#     1. parse "Mutation_Class" information from the "Variant_Classification"
#        column (also named "Mutation_Type" in some files)
#     2. parse "AA_position" (amino-acid position) from the "HGVSp_Short" column 
#        (also named "amino_acid_change" in some files) (e.g., p.Q136P)
# ============================================
mutation.dat <- readMAF(maf.file)

# ============================================
# Chart 1
# "default" chart theme
# ============================================
chart.options <- g3Lollipop.theme(theme.name = "default",
                                  title.text = "PIK3CA gene (default theme)")

g3Lollipop(mutation.dat,
           gene.symbol = "PIK3CA",
           plot.options = chart.options,
           output.filename = "default_theme")
#> Factor is set to Mutation_Class
#> legend title is set to Mutation_Class

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3.2 Example 2: visualize genetic mutation data from CSV or TSV file

In this example, we read genetic mutation data from CSV or TSV files, and visualize it using some customized chart options. Note this is equivalent to dark chart theme.

# load data
mutation.csv <- system.file("extdata", "ccle.csv", package = "g3viz")

# ============================================
# read in data
#   "gene.symbol.col"    : column of gene symbol
#   "variant.class.col"  : column of variant class
#   "protein.change.col" : colum of protein change column
# ============================================
mutation.dat <- readMAF(mutation.csv,
                        gene.symbol.col = "Hugo_Symbol",
                        variant.class.col = "Variant_Classification",
                        protein.change.col = "amino_acid_change",
                        sep = ",")  # column-separator of csv file

# set up chart options
plot.options <- g3Lollipop.options(
  # Chart settings
  chart.width = 600,
  chart.type = "pie",
  chart.margin = list(left = 30, right = 20, top = 20, bottom = 30),
  chart.background = "#d3d3d3",
  transition.time = 300,
  # Lollipop track settings
  lollipop.track.height = 200,
  lollipop.track.background = "#d3d3d3",
  lollipop.pop.min.size = 1,
  lollipop.pop.max.size = 8,
  lollipop.pop.info.limit = 5.5,
  lollipop.pop.info.dy = "0.24em",
  lollipop.pop.info.color = "white",
  lollipop.line.color = "#a9A9A9",
  lollipop.line.width = 3,
  lollipop.circle.color = "#ffdead",
  lollipop.circle.width = 0.4,
  lollipop.label.ratio = 2,
  lollipop.label.min.font.size = 12,
  lollipop.color.scheme = "dark2",
  highlight.text.angle = 60,
  # Domain annotation track settings
  anno.height = 16,
  anno.margin = list(top = 0, bottom = 0),
  anno.background = "#d3d3d3",
  anno.bar.fill = "#a9a9a9",
  anno.bar.margin = list(top = 4, bottom = 4),
  domain.color.scheme = "pie5",
  domain.margin = list(top = 2, bottom = 2),
  domain.text.color = "white",
  domain.text.font = "italic 8px Serif",
  # Y-axis label
  y.axis.label = "# of TP53 gene mutations",
  axis.label.color = "#303030",
  axis.label.alignment = "end",
  axis.label.font = "italic 12px Serif",
  axis.label.dy = "-1.5em",
  y.axis.line.color = "#303030",
  y.axis.line.width = 0.5,
  y.axis.line.style = "line",
  y.max.range.ratio = 1.1,
  # Chart title settings
  title.color = "#303030",
  title.text = "TP53 gene (customized chart options)",
  title.font = "bold 12px monospace",
  title.alignment = "start",
  # Chart legend settings
  legend = TRUE,
  legend.margin = list(left=20, right = 0, top = 10, bottom = 5),
  legend.interactive = TRUE,
  legend.title = "Variant classification",
  # Brush selection tool
  brush = TRUE,
  brush.selection.background = "#F8F8FF",
  brush.selection.opacity = 0.3,
  brush.border.color = "#a9a9a9",
  brush.border.width = 1,
  brush.handler.color = "#303030",
  # tooltip and zoom
  tooltip = TRUE,
  zoom = TRUE
)

g3Lollipop(mutation.dat,
           gene.symbol = "TP53",
           protein.change.col = "amino_acid_change",
           btn.style = "blue", # blue-style chart download buttons
           plot.options = plot.options,
           output.filename = "customized_plot")
#> Factor is set to Mutation_Class

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3.3 Example 3: visualize genetic mutation data from cBioPortal

cBioPortal provides download for many cancer genomics data sets. g3viz has a convenient way to retrieve data directly from this portal.

In this example, we first retrieve genetic mutation data of TP53 gene for the msk_impact_2017 study, and then visualize the data using the built-in cbioportal theme, to miminc cBioPortal’s mutation_mapper.

# Retrieve mutation data of "msk_impact_2017" from cBioPortal
mutation.dat <- getMutationsFromCbioportal("msk_impact_2017", "TP53")
#> Found study msk_impact_2017
#> Found mutation data set msk_impact_2017_mutations
#> 10945 cases in this study

# "cbioportal" chart theme
plot.options <- g3Lollipop.theme(theme.name = "cbioportal",
                                 title.text = "TP53 gene (cbioportal theme)",
                                 y.axis.label = "# of TP53 Mutations")

g3Lollipop(mutation.dat,
           gene.symbol = "TP53",
           btn.style = "gray", # gray-style chart download buttons
           plot.options = plot.options,
           output.filename = "cbioportal_theme")
#> Factor is set to Mutation_Class
#> legend title is set to Mutation_Class

3.3.0.1 Note:

• Internet access is required to download data from cBioPortal. This may take more than 10 seconds, or sometimes it may fail.
• To check what studies are available on cBioPortal

# Connect to CGDS (cancer Genomics Data Server)
cgds <- cgdsr::CGDS("http://www.cbioportal.org/")

# Test if connection is OK
cgdsr::test(cgds)

# To list all studies
all.studies <- cgdsr::getCancerStudies(cgds)

# Pick up a cancer study with mutation data
mutation.dat <- g3viz::getMutationsFromCbioportal("all_stjude_2016", "TP53")

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4 Usage

4.1 Read data

In g3viz, annotated mutation data can be loaded in three ways

1. from MAF file, as in Example 1.

2. from CSV or TSV files, as in Example 2.

3. from cBioPortal (internet access required), as in Example 3.

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4.2 Map mutation type to mutation class

In addtion to reading mutation data, readMAF or getMutationFromCbioportal functions also map mutation type to mutation class and generate a Mutation_Class column by default. Mutation type is usually in the column of Variant_Classification or Mutation_Type. The default mapping table is,

Mutation_Type	Mutation_Class	Short_Name
Inframe
In_Frame_Del	Inframe	IF del
In_Frame_Ins	Inframe	IF ins
Silent	Inframe	Silent
Targeted_Region	Inframe	IF
Missense
Missense_Mutation	Missense	Missense
Truncating
Frame_Shift	Truncating	FS
Frame_Shift_Del	Truncating	FS del
Frame_Shift_Ins	Truncating	FS ins
Nonsense_Mutation	Truncating	Nonsense
Nonstop_Mutation	Truncating	Nonstop
Splice_Region	Truncating	Splice
Splice_Site	Truncating	Splice
Other
3’Flank	Other	3’Flank
3’UTR	Other	3’UTR
5’Flank	Other	5’Flank
5’UTR	Other	5’UTR
De_novo_Start_InFrame	Other	de_novo_start_inframe
De_novo_Start_OutOfFrame	Other	de_novo_start_outofframe
Fusion	Other	Fusion
IGR	Other	IGR
Intron	Other	Intron
lincRNA	Other	lincRNA
RNA	Other	RNA
Start_Codon_Del	Other	Nonstart
Start_Codon_Ins	Other	start_codon_ins
Start_Codon_SNP	Other	Nonstart
Translation_Start_Site	Other	TSS
Unknown	Other	Unknown

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4.3 Retrieve Pfam domain inforamtion

Given a HUGO gene symbol, users can either use hgnc2pfam function to retrieve Pfam protein domain information first or use all-in-one g3Lollipop function to directly create lollipop-diagram. In case that the given gene has multiple isoforms, hgnc2pfam returns all UniProt entries, and users can specify one using the corresponding UniProt entry. If attribute guess is TRUE, the Pfam domain information of the longest UniProt entry is returned.

# Example 1: TP53 has single UniProt entry
hgnc2pfam("TP53", output.format = "list")
#> $symbol
#> [1] "TP53"
#> 
#> $uniprot
#> [1] "P04637"
#> 
#> $length
#> [1] 393
#> 
#> $pfam
#>       hmm.acc     hmm.name start end   type
#> 26656 PF08563      P53_TAD     6  30  Motif
#> 26653 PF18521         TAD2    35  59 Domain
#> 26655 PF00870          P53    99 289 Domain
#> 26654 PF07710 P53_tetramer   319 358  Motif

# Example 2: GNAS has multiple UniProt entries
#   `guess = TRUE`: the Pfam domain information of the longest 
#                   UniProt protein is returned
hgnc2pfam("GNAS", guess = TRUE)
#> GNAS maps to multiple UniProt entries: 
#>  symbol uniprot length
#>    GNAS  O95467    245
#>    GNAS  P63092    394
#>    GNAS  P84996    626
#>    GNAS  Q5JWF2   1037
#> Warning in hgnc2pfam("GNAS", guess = TRUE): Pick: Q5JWF2
#> {"symbol":"GNAS","uniprot":"Q5JWF2","length":1037,"pfam":[{"hmm.acc":"PF00503","hmm.name":"G-alpha","start":663,"end":1026,"type":"Domain"}]}

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4.4 Chart themes

The g3viz package contains 8 ready-to-use chart schemes: default, blue, simple, cbioportal, nature, nature2, ggplot2, and dark. Check this tutorial for examples and usage.

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4.5 Color schemes

Figure 1 demonstrates all color schemes that g3viz supports for lollipop-pops and Pfam domains. More demos are available at demo 1, demo 2, and demo 3.

Figure 1. List of color schemes supported by g3viz

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4.6 Chart options

Chart options can be specified using g3Lollipop.options() function (see example 2). Here is the full list of chart options,

Chart options of g3viz

Option	Description
Chart settings
chart.width	chart width in px. Default 800.
chart.type	pop type, pie or circle. Default pie.
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	chart animation transition time in millisecond. Default 600.
Lollipop track settings
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 in px. Default 2.
lollipop.pop.max.size	lollipop pop maximal size in px. 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. Check color schemes for details.
highlight.text.angle	the rotation angle of on-click highlight text in degree. Default 90.
Domain annotation track settings
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. Check color schemes for details.
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.
Y-axis settings
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.
Chart title settings
title.text	title of chart. Default "".
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.
Chart legend settings
legend	if show legend. Default TRUE.
legend.margin	legend margin in list format. Default list(left = 10, right = 0, top = 5, bottom = 5).
legend.interactive	legend interactive mode. Default TRUE.
legend.title	legend title. If NA, use factor name as factor.col. Default is NA.
Brush selection tool settings
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.
Tooltip and zoom tools
tooltip	if show tooltip. Default TRUE.
zoom	if enable zoom feature. Default TRUE.

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4.7 Save chart as HTML

g3Lollipop also renders two buttons over the lollipop-diagram, allowing to save the resulting chart in PNG or vector-based SVG file. To save chart programmatically as HTML, you can use htmlwidgets::saveWidget function.

chart <- g3Lollipop(mutation.dat,
                    gene.symbol = "TP53",
                    protein.change.col = "amino_acid_change",
                    plot.options = plot.options)
htmlwidgets::saveWidget(chart, "g3lollipop_chart.html")

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5 Session Info

sessionInfo()
#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Catalina 10.15.6
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] kableExtra_1.1.0 knitr_1.29       cgdsr_1.3.0      g3viz_1.1.3     
#> 
#> loaded via a namespace (and not attached):
#>  [1] Rcpp_1.0.5        highr_0.8         compiler_4.0.2    pillar_1.4.6     
#>  [5] R.methodsS3_1.8.0 tools_4.0.2       digest_0.6.25     jsonlite_1.7.0   
#>  [9] evaluate_0.14     tibble_3.0.3      lifecycle_0.2.0   viridisLite_0.3.0
#> [13] pkgconfig_2.0.3   rlang_0.4.7       rstudioapi_0.11   curl_4.3         
#> [17] yaml_2.2.1        xfun_0.16         stringr_1.4.0     httr_1.4.2       
#> [21] xml2_1.3.2        vctrs_0.3.2       htmlwidgets_1.5.1 hms_0.5.3        
#> [25] webshot_0.5.2     glue_1.4.1        R6_2.4.1          rmarkdown_2.3    
#> [29] readr_1.3.1       magrittr_1.5      scales_1.1.1      htmltools_0.5.0  
#> [33] ellipsis_0.3.1    rvest_0.3.6       colorspace_1.4-1  stringi_1.4.6    
#> [37] munsell_0.5.0     crayon_1.3.4      R.oo_1.23.0

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