diff --git a/DESCRIPTION b/DESCRIPTION index cc757f6..4201f3e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -14,6 +14,18 @@ Authors@R: c( family = "Zhang", email = "g3viz.group@gmail.com", role = c("ctb") + ), + person( + given = "Ruining", + family = "Zhu", + email = "g3viz.group@gmail.com", + role = c("ctb") + ), + person( + given = "Feng", + family = "Zhao", + email = "g3viz.group@gmail.com", + role = c("ctb") )) Maintainer: Xin Guo Description: Interface for 'g3-lollipop' 'JavaScript' library. @@ -22,7 +34,7 @@ License: MIT + file LICENSE Encoding: UTF-8 LazyData: true Depends: - R (>= 3.5.0) + R (>= 4.2.0) biocViews: Imports: jsonlite, diff --git a/NEWS.md b/NEWS.md index d10842c..09490dd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +## Version 1.2.0 + - Updated Pfam (v37.0) (date: 2024-07-29) + - Updated UniProtKB (date: 2024-07-29) + ## Version 1.15 (2022/06/30) - Updated `hgnc2pfam.df.rda` data - Remove cgdsr dependencies; add cBioPortalData as the substitution diff --git a/R/getMutationsFromCbioportal.R b/R/getMutationsFromCbioportal.R index 9fa4466..5a26662 100644 --- a/R/getMutationsFromCbioportal.R +++ b/R/getMutationsFromCbioportal.R @@ -53,11 +53,32 @@ getMutationsFromCbioportal <- function(study.id, # ======================== # server - cbio <- cBioPortal() + # cbio <- cBioPortal() + # cbio <- suppressWarnings({ + # cBioPortal( + # hostname = "www.cbioportal.org", + # protocol = "https", + # api. = "/api/v2/api-docs" + # ) + # }) + + cbio <- tryCatch({ + cBioPortal( + hostname = "www.cbioportal.org", + protocol = "https", + api. = "/api/v2/api-docs" + ) + }, warning = function(w){ + # message(w) + }, error = function(e){ + stop("Connection error: can not connect to cBioPortal API") + }, finally = { + # + }) # ======================== # get study information - genetic.profiles <- molecularProfiles(cbio,studyId = study.id) + genetic.profiles <- molecularProfiles(cbio, studyId = study.id) message("Found study ", study.id) # ======================== @@ -71,7 +92,6 @@ getMutationsFromCbioportal <- function(study.id, message("Found mutation data set ", mutation.profile) # ======================== - case.list.details <- sampleLists(cbio, study.id) mutation.case.list.id <- case.list.details$sampleListId diff --git a/docs/chart_themes.html b/docs/chart_themes.html deleted file mode 100644 index 9b22c89..0000000 --- a/docs/chart_themes.html +++ /dev/null @@ -1,2838 +0,0 @@ - - - - - - - - - - - - - - - -G3viz: chart themes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - -
-
-
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-
- -
- - - - - - - -

The g3viz package contains 8 ready-to-use chart schemes: -default, blue, simple, cbioportal, -nature, nature2, ggplot2, and -dark.

-
# read data
-mutation.dat <- readMAF("tables/tp53-msk_impact_2017.tsv", sep="\t")
-
-

1 default -theme

-
chart.options = g3Lollipop.theme(
-      theme.name = "default",
-      title.text = "default theme title",
-      y.axis.label = "y-label",
-      legend.title = "legend-title")
-
-g3Lollipop(mutation.dat,
-           plot.options = chart.options,
-           btn.style = "blue",
-           gene.symbol = "TP53")
-#> Factor is set to Mutation_Class
-
- -
-
-

2 blue -theme

-
g3Lollipop(mutation.dat,
-           plot.options =
-             g3Lollipop.theme(theme.name = "blue",
-                              title.text = "blue theme title",
-                              y.axis.label = "y-label",
-                              legend.title = "legend-title"),
-           btn.style = "blue",
-           gene.symbol = "TP53")
-#> Factor is set to Mutation_Class
-
- -
-
-

3 simple -theme

-
g3Lollipop(mutation.dat,
-           plot.options =
-             g3Lollipop.theme(theme.name = "simple",
-                              title.text = "simple theme title",
-                              y.axis.label = "y-label",
-                              legend.title = "legend-title"),
-           btn.style = "blue",
-           gene.symbol = "TP53")
-#> Factor is set to Mutation_Class
-
- -
-
-

4 cbioportal -theme

-
g3Lollipop(mutation.dat,
-           plot.options =
-             g3Lollipop.theme(theme.name = "cbioportal",
-                              title.text = "cbioportal theme title",
-                              y.axis.label = "y-label",
-                              legend.title = "legend-title"),
-           btn.style = "blue",
-           gene.symbol = "TP53")
-#> Factor is set to Mutation_Class
-
- -
-
-

5 nature -theme

-
g3Lollipop(mutation.dat,
-           plot.options =
-             g3Lollipop.theme(theme.name = "nature",
-                              title.text = "nature theme title",
-                              y.axis.label = "y-label",
-                              legend.title = "legend-title"),
-           btn.style = "blue",
-           gene.symbol = "TP53")
-#> Factor is set to Mutation_Class
-
- -
-
-

6 nature2 -theme

-

-g3Lollipop(mutation.dat,
-           plot.options =
-             g3Lollipop.theme(theme.name = "nature2",
-                              title.text = "nature2 theme title",
-                              y.axis.label = "y-label",
-                              legend.title = "legend-title"),
-           btn.style = "blue",
-           gene.symbol = "TP53")
-#> Factor is set to Mutation_Class
-
- -
-
-

7 ggplot2 -theme

-
g3Lollipop(mutation.dat,
-           plot.options =
-             g3Lollipop.theme(theme.name = "ggplot2",
-                              title.text = "ggplot2 theme title",
-                              y.axis.label = "y-label",
-                              legend.title = "legend-title"),
-           btn.style = "blue",
-           gene.symbol = "TP53")
-#> Factor is set to Mutation_Class
-
- -
-
-

8 dark -theme

-
g3Lollipop(mutation.dat,
-           plot.options =
-             g3Lollipop.theme(theme.name = "dark",
-                              title.text = "dark theme title",
-                              y.axis.label = "y-label",
-                              legend.title = "legend-title"),
-           btn.style = "blue",
-           gene.symbol = "TP53")
-#> Factor is set to Mutation_Class
-
- -
- - - -
-
- -
- - - - - - - - - - - - - - - - diff --git a/docs/index.html b/docs/index.html deleted file mode 100644 index 2a6892e..0000000 --- a/docs/index.html +++ /dev/null @@ -1,4227 +0,0 @@ - - - - - - - - - - - - - - - -G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - -
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- - - - - - - -
-

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

- -

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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
    • -
-

-# list all studies of cBioPortal
-all.studies <- getStudies(cbio, buildReport = FALSE)
-
-# Pick up a cancer study (studyId) with mutation data (gene symbol)
-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. -

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

    3. -

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

    4. -
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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
-#> 14773 PF08563      P53_TAD     6  30  Motif
-#> 14772 PF18521         TAD2    35  59  Motif
-#> 14770 PF00870          P53    99 289 Domain
-#> 14771 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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-
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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` -

-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

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sessionInfo()
-#> R version 4.4.0 (2024-04-24)
-#> Platform: x86_64-apple-darwin20
-#> Running under: macOS Sonoma 14.5
-#> 
-#> Matrix products: default
-#> BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
-#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
-#> 
-#> locale:
-#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
-#> 
-#> time zone: America/Los_Angeles
-#> tzcode source: internal
-#> 
-#> attached base packages:
-#> [1] stats4    stats     graphics  grDevices utils     datasets  methods   base     
-#> 
-#> other attached packages:
-#>  [1] g3viz_1.2.0                 kableExtra_1.4.0            knitr_1.47                  cBioPortalData_2.16.0      
-#>  [5] MultiAssayExperiment_1.30.2 SummarizedExperiment_1.34.0 Biobase_2.64.0              GenomicRanges_1.56.1       
-#>  [9] GenomeInfoDb_1.40.1         IRanges_2.38.0              S4Vectors_0.42.0            BiocGenerics_0.50.0        
-#> [13] MatrixGenerics_1.16.0       matrixStats_1.3.0           AnVIL_1.16.0                dplyr_1.1.4                
-#> [17] rmarkdown_2.27             
-#> 
-#> loaded via a namespace (and not attached):
-#>   [1] rstudioapi_0.16.0         jsonlite_1.8.8            magrittr_2.0.3            GenomicFeatures_1.56.0   
-#>   [5] fs_1.6.4                  BiocIO_1.14.0             zlibbioc_1.50.0           vctrs_0.6.5              
-#>   [9] memoise_2.0.1             Rsamtools_2.20.0          RCurl_1.98-1.14           usethis_2.2.3            
-#>  [13] htmltools_0.5.8.1         S4Arrays_1.4.1            BiocBaseUtils_1.6.0       lambda.r_1.2.4           
-#>  [17] curl_5.2.1                SparseArray_1.4.8         sass_0.4.9                bslib_0.7.0              
-#>  [21] desc_1.4.3                htmlwidgets_1.6.4         testthat_3.2.1.1          futile.options_1.0.1     
-#>  [25] cachem_1.1.0              GenomicAlignments_1.40.0  mime_0.12                 lifecycle_1.0.4          
-#>  [29] pkgconfig_2.0.3           Matrix_1.7-0              R6_2.5.1                  fastmap_1.2.0            
-#>  [33] rcmdcheck_1.4.0           GenomeInfoDbData_1.2.12   shiny_1.8.1.1             digest_0.6.36            
-#>  [37] colorspace_2.1-0          RaggedExperiment_1.28.0   ps_1.7.7                  AnnotationDbi_1.66.0     
-#>  [41] rprojroot_2.0.4           pkgload_1.4.0             RSQLite_2.3.7             filelock_1.0.3           
-#>  [45] RTCGAToolbox_2.34.0       fansi_1.0.6               RJSONIO_1.3-1.9           httr_1.4.7               
-#>  [49] abind_1.4-5               compiler_4.4.0            remotes_2.5.0             withr_3.0.0              
-#>  [53] bit64_4.0.5               BiocParallel_1.38.0       DBI_1.2.3                 pkgbuild_1.4.4           
-#>  [57] highr_0.11                sessioninfo_1.2.2         rappdirs_0.3.3            DelayedArray_0.30.1      
-#>  [61] rjson_0.2.21              tools_4.4.0               httpuv_1.6.15             glue_1.7.0               
-#>  [65] callr_3.7.6               restfulr_0.0.15           promises_1.3.0            grid_4.4.0               
-#>  [69] generics_0.1.3            tzdb_0.4.0                tidyr_1.3.1               data.table_1.15.4        
-#>  [73] hms_1.1.3                 xml2_1.3.6                utf8_1.2.4                XVector_0.44.0           
-#>  [77] pillar_1.9.0              stringr_1.5.1             later_1.3.2               BiocFileCache_2.12.0     
-#>  [81] lattice_0.22-6            rtracklayer_1.64.0        bit_4.0.5                 tidyselect_1.2.1         
-#>  [85] Biostrings_2.72.1         miniUI_0.1.1.1            svglite_2.1.3             futile.logger_1.4.3      
-#>  [89] xfun_0.45                 brio_1.1.5                devtools_2.4.5            DT_0.33                  
-#>  [93] stringi_1.8.4             UCSC.utils_1.0.0          xopen_1.0.1               yaml_2.3.8               
-#>  [97] evaluate_0.24.0           codetools_0.2-20          tibble_3.2.1              cli_3.6.3                
-#> [101] systemfonts_1.1.0         xtable_1.8-4              processx_3.8.4            roxygen2_7.3.2           
-#> [105] munsell_0.5.1             jquerylib_0.1.4           Rcpp_1.0.12               GenomicDataCommons_1.28.0
-#> [109] dbplyr_2.5.0              png_0.1-8                 XML_3.99-0.17             rapiclient_0.1.5         
-#> [113] parallel_4.4.0            ellipsis_0.3.2            TCGAutils_1.24.0          readr_2.1.5              
-#> [117] blob_1.2.4                prettyunits_1.2.0         profvis_0.3.8             urlchecker_1.0.1         
-#> [121] bitops_1.0-7              viridisLite_0.4.2         scales_1.3.0              purrr_1.0.2              
-#> [125] crayon_1.5.3              rlang_1.1.4               KEGGREST_1.44.1           rvest_1.0.4              
-#> [129] formatR_1.14
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- - - - - - - - - - - - - - - - diff --git a/docs/introduction.tex b/docs/introduction.tex deleted file mode 100644 index 4729b69..0000000 --- a/docs/introduction.tex +++ /dev/null @@ -1,779 +0,0 @@ -% Options for packages loaded elsewhere -\PassOptionsToPackage{unicode}{hyperref} -\PassOptionsToPackage{hyphens}{url} -% -\documentclass[ -]{article} -\usepackage{amsmath,amssymb} -\usepackage{iftex} -\ifPDFTeX - \usepackage[T1]{fontenc} - \usepackage[utf8]{inputenc} - \usepackage{textcomp} % provide euro and other symbols -\else % if luatex or xetex - \usepackage{unicode-math} % this also loads fontspec - \defaultfontfeatures{Scale=MatchLowercase} - \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1} -\fi -\usepackage{lmodern} -\ifPDFTeX\else - % xetex/luatex font selection -\fi -% Use upquote if available, for straight quotes in verbatim environments -\IfFileExists{upquote.sty}{\usepackage{upquote}}{} -\IfFileExists{microtype.sty}{% use microtype if available - \usepackage[]{microtype} - \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts -}{} -\makeatletter -\@ifundefined{KOMAClassName}{% if non-KOMA class - \IfFileExists{parskip.sty}{% - \usepackage{parskip} - }{% else - \setlength{\parindent}{0pt} - \setlength{\parskip}{6pt plus 2pt minus 1pt}} -}{% if KOMA class - \KOMAoptions{parskip=half}} -\makeatother -\usepackage{xcolor} -\usepackage[margin=1in]{geometry} -\usepackage{color} -\usepackage{fancyvrb} -\newcommand{\VerbBar}{|} -\newcommand{\VERB}{\Verb[commandchars=\\\{\}]} -\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}} -% Add ',fontsize=\small' for more characters per line -\usepackage{framed} -\definecolor{shadecolor}{RGB}{248,248,248} -\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}} -\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}} -\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}} -\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}} -\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}} -\newcommand{\BuiltInTok}[1]{#1} -\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}} -\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}} -\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}} -\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}} -\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}} -\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}} -\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}} -\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}} -\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}} -\newcommand{\ExtensionTok}[1]{#1} -\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}} -\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}} -\newcommand{\ImportTok}[1]{#1} -\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}} -\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}} -\newcommand{\NormalTok}[1]{#1} -\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}} -\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}} -\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}} -\newcommand{\RegionMarkerTok}[1]{#1} -\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}} -\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}} -\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}} -\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}} -\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}} -\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}} -\usepackage{graphicx} -\makeatletter -\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi} -\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi} -\makeatother -% Scale images if necessary, so that they will not overflow the page -% margins by default, and it is still possible to overwrite the defaults -% using explicit options in \includegraphics[width, height, ...]{} -\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio} -% Set default figure placement to htbp -\makeatletter -\def\fps@figure{htbp} -\makeatother -\setlength{\emergencystretch}{3em} % prevent overfull lines -\providecommand{\tightlist}{% - \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}} -\setcounter{secnumdepth}{-\maxdimen} % remove section numbering -\usepackage{booktabs} -\usepackage{longtable} -\usepackage{array} -\usepackage{multirow} -\usepackage{wrapfig} -\usepackage{float} -\usepackage{colortbl} -\usepackage{pdflscape} -\usepackage{tabu} -\usepackage{threeparttable} -\usepackage{threeparttablex} -\usepackage[normalem]{ulem} -\usepackage{makecell} -\usepackage{xcolor} -\ifLuaTeX - \usepackage{selnolig} % disable illegal ligatures -\fi -\usepackage{bookmark} -\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available -\urlstyle{same} -\hypersetup{ - pdftitle={G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram}, - pdfauthor={g3viz development group \textless g3viz.group at gmail.com\textgreater{}}, - hidelinks, - pdfcreator={LaTeX via pandoc}} - -\title{G3viz: an R package to interactively visualize genetic mutation -data using a lollipop-diagram} -\author{g3viz development group \textless g3viz.group at -gmail.com\textgreater{}} -\date{2024-07-28} - -\begin{document} -\maketitle - -\section{Introduction}\label{introduction} - -Intuitively and effectively visualizing genetic mutation data can help -researchers to better understand genomic data and validate findings. -\texttt{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 \texttt{g3viz} include - -\begin{itemize} -\tightlist -\item - Interactive (zoom \& pan, tooltip, brush selection tool, and - interactive legend) -\item - Highlight and label positional mutations -\item - 8 ready-to-use \hyperref[themes]{chart themes} -\item - Highly customizable with over 50 \hyperref[options]{chart options} and - over 35 \hyperref[schemes]{color schemes} -\item - Save charts in PNG or high-quality SVG format -\item - Built-in function to retrieve \hyperref[pfam]{protein domain - information} and resolve gene isoforms -\item - Built-in function to \hyperref[mutation]{map genetic mutation type - (a.k.a, variant classification) to mutation class} -\end{itemize} - -\hyperref[top]{↥ back to top} - -\section{\texorpdfstring{Install -\texttt{g3viz}}{Install g3viz}}\label{install-g3viz} - -Install from R repository - -\begin{Shaded} -\begin{Highlighting}[] -\CommentTok{\# install package} -\FunctionTok{install.packages}\NormalTok{(}\StringTok{"g3viz"}\NormalTok{, }\AttributeTok{repos =} \StringTok{"http://cran.us.r{-}project.org"}\NormalTok{)} -\end{Highlighting} -\end{Shaded} - -or install development version from github - -\begin{Shaded} -\begin{Highlighting}[] -\CommentTok{\# Check if "devtools" installed} -\ControlFlowTok{if}\NormalTok{(}\StringTok{"devtools"} \SpecialCharTok{\%in\%} \FunctionTok{rownames}\NormalTok{(}\FunctionTok{installed.packages}\NormalTok{()) }\SpecialCharTok{==} \ConstantTok{FALSE}\NormalTok{)\{ } - \FunctionTok{install.packages}\NormalTok{(}\StringTok{"devtools"}\NormalTok{)} -\NormalTok{\}} - -\CommentTok{\# install from github} -\NormalTok{devtools}\SpecialCharTok{::}\FunctionTok{install\_github}\NormalTok{(}\StringTok{"g3viz/g3viz"}\NormalTok{)} -\end{Highlighting} -\end{Shaded} - -\hyperref[top]{↥ back to top} - -\section{Quick Start}\label{quick-start} - -\begin{Shaded} -\begin{Highlighting}[] -\CommentTok{\# load g3viz package} -\FunctionTok{library}\NormalTok{(g3viz)} -\end{Highlighting} -\end{Shaded} - -\subsection{\texorpdfstring{Example 1: Visualize genetic mutation data -from \texttt{MAF} -file}{Example 1: Visualize genetic mutation data from MAF file}}\label{example-1-visualize-genetic-mutation-data-from-maf-file} - -Mutation Annotation Format -(\href{https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/}{MAF}) -is a commonly-used tab-delimited text file for storing aggregated -mutation information. It could be generated from -\href{https://docs.gdc.cancer.gov/Data/File_Formats/VCF_Format/}{VCF} -file using tools like \href{https://github.com/mskcc/vcf2maf}{vcf2maf}. -Translational effect of variant alleles in \texttt{MAF} files are -usually in the column named \texttt{Variant\_Classification} or -\texttt{Mutation\_Type} (\emph{i.e.}, \texttt{Frame\_Shift\_Del}, -\texttt{Split\_Site}). In this example, the somatic mutation data of the -\emph{TCGA-BRCA} study was originally downloaded from the -\href{https://portal.gdc.cancer.gov/projects/TCGA-BRCA}{GDC Data -Portal}. - -\begin{Shaded} -\begin{Highlighting}[] -\CommentTok{\# System file} -\NormalTok{maf.file }\OtherTok{\textless{}{-}} \FunctionTok{system.file}\NormalTok{(}\StringTok{"extdata"}\NormalTok{, }\StringTok{"TCGA.BRCA.varscan.somatic.maf.gz"}\NormalTok{, }\AttributeTok{package =} \StringTok{"g3viz"}\NormalTok{)} - -\CommentTok{\# ============================================} -\CommentTok{\# Read in MAF file} -\CommentTok{\# In addition to read data in, g3viz::readMAF function does} -\CommentTok{\# 1. parse "Mutation\_Class" information from the "Variant\_Classification"} -\CommentTok{\# column (also named "Mutation\_Type" in some files)} -\CommentTok{\# 2. parse "AA\_position" (amino{-}acid position) from the "HGVSp\_Short" column } -\CommentTok{\# (also named "amino\_acid\_change" in some files) (e.g., p.Q136P)} -\CommentTok{\# ============================================} -\NormalTok{mutation.dat }\OtherTok{\textless{}{-}} \FunctionTok{readMAF}\NormalTok{(maf.file)} -\end{Highlighting} -\end{Shaded} - -\begin{Shaded} -\begin{Highlighting}[] -\CommentTok{\# ============================================} -\CommentTok{\# Chart 1} -\CommentTok{\# "default" chart theme} -\CommentTok{\# ============================================} -\NormalTok{chart.options }\OtherTok{\textless{}{-}} \FunctionTok{g3Lollipop.theme}\NormalTok{(}\AttributeTok{theme.name =} \StringTok{"default"}\NormalTok{,} - \AttributeTok{title.text =} \StringTok{"PIK3CA gene (default theme)"}\NormalTok{)} - -\FunctionTok{g3Lollipop}\NormalTok{(mutation.dat,} - \AttributeTok{gene.symbol =} \StringTok{"PIK3CA"}\NormalTok{,} - \AttributeTok{plot.options =}\NormalTok{ chart.options,} - \AttributeTok{output.filename =} \StringTok{"default\_theme"}\NormalTok{)} -\CommentTok{\#\textgreater{} Factor is set to Mutation\_Class} -\CommentTok{\#\textgreater{} legend title is set to Mutation\_Class} -\end{Highlighting} -\end{Shaded} - -\includegraphics{/Users/xguo/Projects/RESEARCH/g3viz/docs/introduction_files/figure-latex/unnamed-chunk-4-1.pdf} - -\hyperref[top]{↥ back to top} - -\subsection{\texorpdfstring{Example 2: visualize genetic mutation data -from \texttt{CSV} or \texttt{TSV} -file}{Example 2: visualize genetic mutation data from CSV or TSV file}}\label{example-2-visualize-genetic-mutation-data-from-csv-or-tsv-file} - -In this example, we read genetic mutation data from \texttt{CSV} or -\texttt{TSV} files, and visualize it using some customized -\hyperref[options]{chart options}. Note this is equivalent to -\emph{dark} chart theme. - -\begin{Shaded} -\begin{Highlighting}[] -\CommentTok{\# load data} -\NormalTok{mutation.csv }\OtherTok{\textless{}{-}} \FunctionTok{system.file}\NormalTok{(}\StringTok{"extdata"}\NormalTok{, }\StringTok{"ccle.csv"}\NormalTok{, }\AttributeTok{package =} \StringTok{"g3viz"}\NormalTok{)} - -\CommentTok{\# ============================================} -\CommentTok{\# read in data} -\CommentTok{\# "gene.symbol.col" : column of gene symbol} -\CommentTok{\# "variant.class.col" : column of variant class} -\CommentTok{\# "protein.change.col" : colum of protein change column} -\CommentTok{\# ============================================} -\NormalTok{mutation.dat }\OtherTok{\textless{}{-}} \FunctionTok{readMAF}\NormalTok{(mutation.csv,} - \AttributeTok{gene.symbol.col =} \StringTok{"Hugo\_Symbol"}\NormalTok{,} - \AttributeTok{variant.class.col =} \StringTok{"Variant\_Classification"}\NormalTok{,} - \AttributeTok{protein.change.col =} \StringTok{"amino\_acid\_change"}\NormalTok{,} - \AttributeTok{sep =} \StringTok{","}\NormalTok{) }\CommentTok{\# column{-}separator of csv file} - -\CommentTok{\# set up chart options} -\NormalTok{plot.options }\OtherTok{\textless{}{-}} \FunctionTok{g3Lollipop.options}\NormalTok{(} - \CommentTok{\# Chart settings} - \AttributeTok{chart.width =} \DecValTok{600}\NormalTok{,} - \AttributeTok{chart.type =} \StringTok{"pie"}\NormalTok{,} - \AttributeTok{chart.margin =} \FunctionTok{list}\NormalTok{(}\AttributeTok{left =} \DecValTok{30}\NormalTok{, }\AttributeTok{right =} \DecValTok{20}\NormalTok{, }\AttributeTok{top =} \DecValTok{20}\NormalTok{, }\AttributeTok{bottom =} \DecValTok{30}\NormalTok{),} - \AttributeTok{chart.background =} \StringTok{"\#d3d3d3"}\NormalTok{,} - \AttributeTok{transition.time =} \DecValTok{300}\NormalTok{,} - \CommentTok{\# Lollipop track settings} - \AttributeTok{lollipop.track.height =} \DecValTok{200}\NormalTok{,} - \AttributeTok{lollipop.track.background =} \StringTok{"\#d3d3d3"}\NormalTok{,} - \AttributeTok{lollipop.pop.min.size =} \DecValTok{1}\NormalTok{,} - \AttributeTok{lollipop.pop.max.size =} \DecValTok{8}\NormalTok{,} - \AttributeTok{lollipop.pop.info.limit =} \FloatTok{5.5}\NormalTok{,} - \AttributeTok{lollipop.pop.info.dy =} \StringTok{"0.24em"}\NormalTok{,} - \AttributeTok{lollipop.pop.info.color =} \StringTok{"white"}\NormalTok{,} - \AttributeTok{lollipop.line.color =} \StringTok{"\#a9A9A9"}\NormalTok{,} - \AttributeTok{lollipop.line.width =} \DecValTok{3}\NormalTok{,} - \AttributeTok{lollipop.circle.color =} \StringTok{"\#ffdead"}\NormalTok{,} - \AttributeTok{lollipop.circle.width =} \FloatTok{0.4}\NormalTok{,} - \AttributeTok{lollipop.label.ratio =} \DecValTok{2}\NormalTok{,} - \AttributeTok{lollipop.label.min.font.size =} \DecValTok{12}\NormalTok{,} - \AttributeTok{lollipop.color.scheme =} \StringTok{"dark2"}\NormalTok{,} - \AttributeTok{highlight.text.angle =} \DecValTok{60}\NormalTok{,} - \CommentTok{\# Domain annotation track settings} - \AttributeTok{anno.height =} \DecValTok{16}\NormalTok{,} - \AttributeTok{anno.margin =} \FunctionTok{list}\NormalTok{(}\AttributeTok{top =} \DecValTok{0}\NormalTok{, }\AttributeTok{bottom =} \DecValTok{0}\NormalTok{),} - \AttributeTok{anno.background =} \StringTok{"\#d3d3d3"}\NormalTok{,} - \AttributeTok{anno.bar.fill =} \StringTok{"\#a9a9a9"}\NormalTok{,} - \AttributeTok{anno.bar.margin =} \FunctionTok{list}\NormalTok{(}\AttributeTok{top =} \DecValTok{4}\NormalTok{, }\AttributeTok{bottom =} \DecValTok{4}\NormalTok{),} - \AttributeTok{domain.color.scheme =} \StringTok{"pie5"}\NormalTok{,} - \AttributeTok{domain.margin =} \FunctionTok{list}\NormalTok{(}\AttributeTok{top =} \DecValTok{2}\NormalTok{, }\AttributeTok{bottom =} \DecValTok{2}\NormalTok{),} - \AttributeTok{domain.text.color =} \StringTok{"white"}\NormalTok{,} - \AttributeTok{domain.text.font =} \StringTok{"italic 8px Serif"}\NormalTok{,} - \CommentTok{\# Y{-}axis label} - \AttributeTok{y.axis.label =} \StringTok{"\# of TP53 gene mutations"}\NormalTok{,} - \AttributeTok{axis.label.color =} \StringTok{"\#303030"}\NormalTok{,} - \AttributeTok{axis.label.alignment =} \StringTok{"end"}\NormalTok{,} - \AttributeTok{axis.label.font =} \StringTok{"italic 12px Serif"}\NormalTok{,} - \AttributeTok{axis.label.dy =} \StringTok{"{-}1.5em"}\NormalTok{,} - \AttributeTok{y.axis.line.color =} \StringTok{"\#303030"}\NormalTok{,} - \AttributeTok{y.axis.line.width =} \FloatTok{0.5}\NormalTok{,} - \AttributeTok{y.axis.line.style =} \StringTok{"line"}\NormalTok{,} - \AttributeTok{y.max.range.ratio =} \FloatTok{1.1}\NormalTok{,} - \CommentTok{\# Chart title settings} - \AttributeTok{title.color =} \StringTok{"\#303030"}\NormalTok{,} - \AttributeTok{title.text =} \StringTok{"TP53 gene (customized chart options)"}\NormalTok{,} - \AttributeTok{title.font =} \StringTok{"bold 12px monospace"}\NormalTok{,} - \AttributeTok{title.alignment =} \StringTok{"start"}\NormalTok{,} - \CommentTok{\# Chart legend settings} - \AttributeTok{legend =} \ConstantTok{TRUE}\NormalTok{,} - \AttributeTok{legend.margin =} \FunctionTok{list}\NormalTok{(}\AttributeTok{left=}\DecValTok{20}\NormalTok{, }\AttributeTok{right =} \DecValTok{0}\NormalTok{, }\AttributeTok{top =} \DecValTok{10}\NormalTok{, }\AttributeTok{bottom =} \DecValTok{5}\NormalTok{),} - \AttributeTok{legend.interactive =} \ConstantTok{TRUE}\NormalTok{,} - \AttributeTok{legend.title =} \StringTok{"Variant classification"}\NormalTok{,} - \CommentTok{\# Brush selection tool} - \AttributeTok{brush =} \ConstantTok{TRUE}\NormalTok{,} - \AttributeTok{brush.selection.background =} \StringTok{"\#F8F8FF"}\NormalTok{,} - \AttributeTok{brush.selection.opacity =} \FloatTok{0.3}\NormalTok{,} - \AttributeTok{brush.border.color =} \StringTok{"\#a9a9a9"}\NormalTok{,} - \AttributeTok{brush.border.width =} \DecValTok{1}\NormalTok{,} - \AttributeTok{brush.handler.color =} \StringTok{"\#303030"}\NormalTok{,} - \CommentTok{\# tooltip and zoom} - \AttributeTok{tooltip =} \ConstantTok{TRUE}\NormalTok{,} - \AttributeTok{zoom =} \ConstantTok{TRUE} -\NormalTok{)} - -\FunctionTok{g3Lollipop}\NormalTok{(mutation.dat,} - \AttributeTok{gene.symbol =} \StringTok{"TP53"}\NormalTok{,} - \AttributeTok{protein.change.col =} \StringTok{"amino\_acid\_change"}\NormalTok{,} - \AttributeTok{btn.style =} \StringTok{"blue"}\NormalTok{, }\CommentTok{\# blue{-}style chart download buttons} - \AttributeTok{plot.options =}\NormalTok{ plot.options,} - \AttributeTok{output.filename =} \StringTok{"customized\_plot"}\NormalTok{)} -\CommentTok{\#\textgreater{} Factor is set to Mutation\_Class} -\end{Highlighting} -\end{Shaded} - -\includegraphics{/Users/xguo/Projects/RESEARCH/g3viz/docs/introduction_files/figure-latex/unnamed-chunk-5-1.pdf} - -\hyperref[top]{↥ back to top} - -\subsection{\texorpdfstring{Example 3: visualize genetic mutation data -from -\texttt{cBioPortal}}{Example 3: visualize genetic mutation data from cBioPortal}}\label{example-3-visualize-genetic-mutation-data-from-cbioportal} - -\href{http://www.cbioportal.org/}{cBioPortal} provides download for many -cancer genomics data sets. \texttt{g3viz} has a convenient way to -retrieve data directly from this portal. - -In this example, we first retrieve genetic mutation data of -\texttt{TP53} gene for the -\href{https://pubmed.ncbi.nlm.nih.gov/28481359/}{msk\_impact\_2017} -study, and then visualize the data using the built-in -\texttt{cbioportal} theme, to miminc cBioPortal's -\href{https://www.cbioportal.org/mutation_mapper}{mutation\_mapper}. - -\begin{Shaded} -\begin{Highlighting}[] -\CommentTok{\# Retrieve mutation data of "msk\_impact\_2017" from cBioPortal} -\NormalTok{mutation.dat }\OtherTok{\textless{}{-}} \FunctionTok{getMutationsFromCbioportal}\NormalTok{(}\StringTok{"msk\_impact\_2017"}\NormalTok{, }\StringTok{"TP53"}\NormalTok{)} -\CommentTok{\#\textgreater{} Found study msk\_impact\_2017} -\CommentTok{\#\textgreater{} Found mutation data set msk\_impact\_2017\_mutations} -\CommentTok{\#\textgreater{} 10945 cases in this study} -\end{Highlighting} -\end{Shaded} - -\begin{Shaded} -\begin{Highlighting}[] - -\CommentTok{\# "cbioportal" chart theme} -\NormalTok{plot.options }\OtherTok{\textless{}{-}} \FunctionTok{g3Lollipop.theme}\NormalTok{(}\AttributeTok{theme.name =} \StringTok{"cbioportal"}\NormalTok{,} - \AttributeTok{title.text =} \StringTok{"TP53 gene (cbioportal theme)"}\NormalTok{,} - \AttributeTok{y.axis.label =} \StringTok{"\# of TP53 Mutations"}\NormalTok{)} - -\FunctionTok{g3Lollipop}\NormalTok{(mutation.dat,} - \AttributeTok{gene.symbol =} \StringTok{"TP53"}\NormalTok{,} - \AttributeTok{btn.style =} \StringTok{"gray"}\NormalTok{, }\CommentTok{\# gray{-}style chart download buttons} - \AttributeTok{plot.options =}\NormalTok{ plot.options,} - \AttributeTok{output.filename =} \StringTok{"cbioportal\_theme"}\NormalTok{)} -\CommentTok{\#\textgreater{} Factor is set to Mutation\_Class} -\CommentTok{\#\textgreater{} legend title is set to Mutation\_Class} -\end{Highlighting} -\end{Shaded} - -\includegraphics{/Users/xguo/Projects/RESEARCH/g3viz/docs/introduction_files/figure-latex/unnamed-chunk-6-1.pdf} - -\paragraph{Note:}\label{note} - -\begin{itemize} -\tightlist -\item - Internet access is required to download data from - \href{http://www.cbioportal.org/}{cBioPortal}. This may take more than - 10 seconds, or sometimes it may fail. -\item - To check what studies are available on cBioPortal -\end{itemize} - -\begin{Shaded} -\begin{Highlighting}[] - -\CommentTok{\# list all studies of cBioPortal} -\NormalTok{all.studies }\OtherTok{\textless{}{-}} \FunctionTok{getStudies}\NormalTok{(cbio, }\AttributeTok{buildReport =} \ConstantTok{FALSE}\NormalTok{)} - -\CommentTok{\# Pick up a cancer study (studyId) with mutation data (gene symbol)} -\NormalTok{mutation.dat }\OtherTok{\textless{}{-}}\NormalTok{ g3viz}\SpecialCharTok{::}\FunctionTok{getMutationsFromCbioportal}\NormalTok{(}\StringTok{"all\_stjude\_2016"}\NormalTok{, }\StringTok{"TP53"}\NormalTok{)} -\end{Highlighting} -\end{Shaded} - -\hyperref[top]{↥ back to top} - -\section{Usage}\label{usage} - -\subsection{Read data}\label{read-data} - -In \texttt{g3viz}, annotated mutation data can be loaded in three ways - -\begin{enumerate} -\def\labelenumi{\arabic{enumi}.} -\item - from - \href{https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/}{MAF} - file, as in \hyperref[ex1]{Example 1}. -\item - from \texttt{CSV} or \texttt{TSV} files, as in \hyperref[ex2]{Example - 2}. -\item - from \href{http://www.cbioportal.org/}{cBioPortal} (internet access - required), as in \hyperref[ex3]{Example 3}. -\end{enumerate} - -\hyperref[top]{↥ back to top} - -\subsection{Map mutation type to mutation -class}\label{map-mutation-type-to-mutation-class} - -In addtion to reading mutation data, \texttt{readMAF} or -\texttt{getMutationFromCbioportal} functions also map mutation type to -mutation class and generate a \texttt{Mutation\_Class} column by -default. Mutation type is usually in the column of -\texttt{Variant\_Classification} or \texttt{Mutation\_Type}. The default -mapping table is, - -\begin{longtabu} to \linewidth {>{\raggedright}X>{\raggedright}X>{\raggedright}X} -\toprule -Mutation\_Type & Mutation\_Class & Short\_Name\\ -\midrule -\addlinespace[0.3em] -\multicolumn{3}{l}{\textbf{Inframe}}\\ -\hspace{1em}In\_Frame\_Del & Inframe & IF del\\ -\hspace{1em}In\_Frame\_Ins & Inframe & IF ins\\ -\hspace{1em}Silent & Inframe & Silent\\ -\hspace{1em}Targeted\_Region & Inframe & IF\\ -\addlinespace[0.3em] -\multicolumn{3}{l}{\textbf{Missense}}\\ -\hspace{1em}Missense\_Mutation & Missense & Missense\\ -\addlinespace[0.3em] -\multicolumn{3}{l}{\textbf{Truncating}}\\ -\hspace{1em}Frame\_Shift & Truncating & FS\\ -\hspace{1em}Frame\_Shift\_Del & Truncating & FS del\\ -\hspace{1em}Frame\_Shift\_Ins & Truncating & FS ins\\ -\hspace{1em}Nonsense\_Mutation & Truncating & Nonsense\\ -\hspace{1em}Nonstop\_Mutation & Truncating & Nonstop\\ -\hspace{1em}Splice\_Region & Truncating & Splice\\ -\hspace{1em}Splice\_Site & Truncating & Splice\\ -\addlinespace[0.3em] -\multicolumn{3}{l}{\textbf{Other}}\\ -\hspace{1em}3’Flank & Other & 3’Flank\\ -\hspace{1em}3’UTR & Other & 3’UTR\\ -\hspace{1em}5’Flank & Other & 5’Flank\\ -\hspace{1em}5’UTR & Other & 5’UTR\\ -\hspace{1em}De\_novo\_Start\_InFrame & Other & de\_novo\_start\_inframe\\ -\hspace{1em}De\_novo\_Start\_OutOfFrame & Other & de\_novo\_start\_outofframe\\ -\hspace{1em}Fusion & Other & Fusion\\ -\hspace{1em}IGR & Other & IGR\\ -\hspace{1em}Intron & Other & Intron\\ -\hspace{1em}lincRNA & Other & lincRNA\\ -\hspace{1em}RNA & Other & RNA\\ -\hspace{1em}Start\_Codon\_Del & Other & Nonstart\\ -\hspace{1em}Start\_Codon\_Ins & Other & start\_codon\_ins\\ -\hspace{1em}Start\_Codon\_SNP & Other & Nonstart\\ -\hspace{1em}Translation\_Start\_Site & Other & TSS\\ -\hspace{1em}Unknown & Other & Unknown\\ -\bottomrule -\end{longtabu} - -\hyperref[top]{↥ back to top} - -\subsection{Retrieve Pfam domain -inforamtion}\label{retrieve-pfam-domain-inforamtion} - -Given a \href{https://www.genenames.org/}{HUGO} gene symbol, users can -either use \texttt{hgnc2pfam} function to retrieve -\href{https://pfam.xfam.org/}{Pfam} protein domain information first or -use all-in-one \texttt{g3Lollipop} function to directly create -lollipop-diagram. In case that the given gene has multiple isoforms, -\texttt{hgnc2pfam} returns all \href{https://www.uniprot.org/}{UniProt} -entries, and users can specify one using the corresponding -\texttt{UniProt} entry. If attribute \texttt{guess} is \texttt{TRUE}, -the Pfam domain information of the longest UniProt entry is returned. - -\begin{Shaded} -\begin{Highlighting}[] -\CommentTok{\# Example 1: TP53 has single UniProt entry} -\FunctionTok{hgnc2pfam}\NormalTok{(}\StringTok{"TP53"}\NormalTok{, }\AttributeTok{output.format =} \StringTok{"list"}\NormalTok{)} -\CommentTok{\#\textgreater{} $symbol} -\CommentTok{\#\textgreater{} [1] "TP53"} -\CommentTok{\#\textgreater{} } -\CommentTok{\#\textgreater{} $uniprot} -\CommentTok{\#\textgreater{} [1] "P04637"} -\CommentTok{\#\textgreater{} } -\CommentTok{\#\textgreater{} $length} -\CommentTok{\#\textgreater{} [1] 393} -\CommentTok{\#\textgreater{} } -\CommentTok{\#\textgreater{} $pfam} -\CommentTok{\#\textgreater{} hmm.acc hmm.name start end type} -\CommentTok{\#\textgreater{} 14773 PF08563 P53\_TAD 6 30 Motif} -\CommentTok{\#\textgreater{} 14772 PF18521 TAD2 35 59 Motif} -\CommentTok{\#\textgreater{} 14770 PF00870 P53 99 289 Domain} -\CommentTok{\#\textgreater{} 14771 PF07710 P53\_tetramer 319 358 Motif} -\end{Highlighting} -\end{Shaded} - -\begin{Shaded} -\begin{Highlighting}[] - -\CommentTok{\# Example 2: GNAS has multiple UniProt entries} -\CommentTok{\# \textasciigrave{}guess = TRUE\textasciigrave{}: the Pfam domain information of the longest } -\CommentTok{\# UniProt protein is returned} -\FunctionTok{hgnc2pfam}\NormalTok{(}\StringTok{"GNAS"}\NormalTok{, }\AttributeTok{guess =} \ConstantTok{TRUE}\NormalTok{)} -\CommentTok{\#\textgreater{} GNAS maps to multiple UniProt entries: } -\CommentTok{\#\textgreater{} symbol uniprot length} -\CommentTok{\#\textgreater{} GNAS O95467 245} -\CommentTok{\#\textgreater{} GNAS P63092 394} -\CommentTok{\#\textgreater{} GNAS P84996 626} -\CommentTok{\#\textgreater{} GNAS Q5JWF2 1037} -\CommentTok{\#\textgreater{} Warning in hgnc2pfam("GNAS", guess = TRUE): Pick: Q5JWF2} -\CommentTok{\#\textgreater{} \{"symbol":"GNAS","uniprot":"Q5JWF2","length":1037,"pfam":[\{"hmm.acc":"PF00503","hmm.name":"G{-}alpha","start":663,"end":1026,"type":"Domain"\}]\}} -\end{Highlighting} -\end{Shaded} - -\hyperref[top]{↥ back to top} - -\subsection{\texorpdfstring{ Chart -themes}{ Chart themes}}\label{chart-themes} - -The \texttt{g3viz} package contains 8 ready-to-use chart schemes: -\emph{default}, \emph{blue}, \emph{simple}, \emph{cbioportal}, -\emph{nature}, \emph{nature2}, \emph{ggplot2}, and \emph{dark}. Check -\href{chart_themes.html}{this tutorial} for examples and usage. - -\hyperref[top]{↥ back to top} - -\subsection{\texorpdfstring{ Color -schemes}{ Color schemes}}\label{color-schemes} - -\hyperref[color_scheme_fig1]{Figure 1} demonstrates all color schemes -that \texttt{g3viz} supports for lollipop-pops and Pfam domains. More -demos are available at -\href{https://bl.ocks.org/phoeguo/raw/2868503a074a6441b5ae6d987f150d48/}{demo -1}, -\href{https://bl.ocks.org/phoeguo/raw/de79b9ce9bda958173af9891ab7aec93/}{demo -2}, and -\href{https://bl.ocks.org/phoeguo/raw/81dffe0c7c6c8caae06f6a5f60c70d19/}{demo -3}. - -\begin{figure} - -{\centering \includegraphics[width=620px]{figures/color_scheme} - -} - -\caption{**Figure 1.** List of color schemes supported by `g3viz`}\label{fig:chunk-label} -\end{figure} - -\hyperref[top]{↥ back to top} - -\subsection{\texorpdfstring{ Chart -options}{ Chart options}}\label{chart-options} - -Chart options can be specified using \texttt{g3Lollipop.options()} -function (see \hyperref[ex2]{example 2}). Here is the full list of chart -options, - -\begin{longtabu} to \linewidth {>{\raggedright}X>{\raggedright}X} -\caption{\label{tab:unnamed-chunk-9}Chart options of `g3viz`}\\ -\toprule -Option & Description\\ -\midrule -\addlinespace[0.3em] -\multicolumn{2}{l}{\textbf{Chart settings}}\\ -\hspace{1em}chart.width & chart width in px. Default `800`.\\ -\hspace{1em}chart.type & pop type, `pie` or `circle`. Default `pie`.\\ -\hspace{1em}chart.margin & specify chart margin in \_list\_ format. Default `list(left = 40, right = 20, top = 15, bottom = 25)`.\\ -\hspace{1em}chart.background & chart background. Default `transparent`.\\ -\hspace{1em}transition.time & chart animation transition time in millisecond. Default `600`.\\ -\addlinespace[0.3em] -\multicolumn{2}{l}{\textbf{Lollipop track settings}}\\ -\hspace{1em}lollipop.track.height & height of lollipop track. Default `420`.\\ -\hspace{1em}lollipop.track.background & background of lollipop track. Default `rgb(244,244,244)`.\\ -\hspace{1em}lollipop.pop.min.size & lollipop pop minimal size in px. Default `2`.\\ -\hspace{1em}lollipop.pop.max.size & lollipop pop maximal size in px. Default `12`.\\ -\hspace{1em}lollipop.pop.info.limit & threshold of lollipop pop size to show count information in middle of pop. Default `8`.\\ -\hspace{1em}lollipop.pop.info.color & lollipop pop information text color. Default `\#EEE`.\\ -\hspace{1em}lollipop.pop.info.dy & y-axis direction text adjustment of lollipop pop information. Default `-0.35em`.\\ -\hspace{1em}lollipop.line.color & lollipop line color. Default `rgb(42,42,42)`.\\ -\hspace{1em}lollipop.line.width & lollipop line width. Default `0.5`.\\ -\hspace{1em}lollipop.circle.color & lollipop circle border color. Default `wheat`.\\ -\hspace{1em}lollipop.circle.width & lollipop circle border width. Default `0.5`.\\ -\hspace{1em}lollipop.label.ratio & lollipop click-out label font size to circle size ratio. Default `1.4`.\\ -\hspace{1em}lollipop.label.min.font.size & lollipop click-out label minimal font size. Default `10`.\\ -\hspace{1em}lollipop.color.scheme & color scheme to fill lollipop pops. Default `accent`. Check [color schemes](\#schemes) for details.\\ -\hspace{1em}highlight.text.angle & the rotation angle of on-click highlight text in degree. Default `90`.\\ -\addlinespace[0.3em] -\multicolumn{2}{l}{\textbf{Domain annotation track settings}}\\ -\hspace{1em}anno.height & height of protein structure annotation track. Default `30`.\\ -\hspace{1em}anno.margin & margin of protein structure annotation track. Default `list(top = 4, bottom = 0)`.\\ -\hspace{1em}anno.background & background of protein structure annotation track. Default `transparent`.\\ -\hspace{1em}anno.bar.fill & background of protein bar in protein structure annotation track. Default `\#E5E3E1`.\\ -\hspace{1em}anno.bar.margin & margin of protein bar in protein structure annotation track. Default `list(top = 2, bottom = 2)`.\\ -\hspace{1em}domain.color.scheme & color scheme of protein domains. Default `category10`. Check [color schemes](\#schemes) for details.\\ -\hspace{1em}domain.margin & margin of protein domains. Default `list(top = 0, bottom = 0)`.\\ -\hspace{1em}domain.text.font & domain label text font in shorthand format. Default `normal 11px Arial`.\\ -\hspace{1em}domain.text.color & domain label text color. Default `\#F2F2F2`.\\ -\addlinespace[0.3em] -\multicolumn{2}{l}{\textbf{Y-axis settings}}\\ -\hspace{1em}y.axis.label & Y-axis label text. Default `\# of mutations`.\\ -\hspace{1em}axis.label.font & css font style shorthand (font-style font-variant font-weight font-size/line-height font-family). Default `normal 12px Arial`.\\ -\hspace{1em}axis.label.color & axis label text color. Default `\#4f4f4f`.\\ -\hspace{1em}axis.label.alignment & axis label text alignment (start/end/middle). Default `middle`\\ -\hspace{1em}axis.label.dy & text adjustment of axis label text. Default `-2em`.\\ -\hspace{1em}y.axis.line.color & color of y-axis in-chart lines (ticks). Default `\#c4c8ca`.\\ -\hspace{1em}y.axis.line.style & style of y-axis in-chart lines (ticks), `dash` or `line`. Default `dash`.\\ -\hspace{1em}y.axis.line.width & width of y-axis in-chart lines (ticks). Default `1`.\\ -\hspace{1em}y.max.range.ratio & ratio of y-axis range to data value range. Default `1.1`.\\ -\addlinespace[0.3em] -\multicolumn{2}{l}{\textbf{Chart title settings}}\\ -\hspace{1em}title.text & title of chart. Default "".\\ -\hspace{1em}title.font & font of chart title. Default `normal 16px Arial`.\\ -\hspace{1em}title.color & color of chart title. Default `\#424242`.\\ -\hspace{1em}title.alignment & text alignment of chart title (start/middle/end). Default `middle`.\\ -\hspace{1em}title.dy & text adjustment of chart title. Default `0.35em`.\\ -\addlinespace[0.3em] -\multicolumn{2}{l}{\textbf{Chart legend settings}}\\ -\hspace{1em}legend & if show legend. Default `TRUE`.\\ -\hspace{1em}legend.margin & legend margin in \_list\_ format. Default `list(left = 10, right = 0, top = 5, bottom = 5)`.\\ -\hspace{1em}legend.interactive & legend interactive mode. Default `TRUE`.\\ -\hspace{1em}legend.title & legend title. If `NA`, use factor name as `factor.col`. Default is `NA`.\\ -\addlinespace[0.3em] -\multicolumn{2}{l}{\textbf{Brush selection tool settings}}\\ -\hspace{1em}brush & if show brush. Default `TRUE`.\\ -\hspace{1em}brush.selection.background & background color of selection brush. Default `\#666`.\\ -\hspace{1em}brush.selection.opacity & background opacity of selection brush. Default `0.2`.\\ -\hspace{1em}brush.border.color & border color of selection brush. Default `\#969696`.\\ -\hspace{1em}brush.handler.color & color of left and right handlers of selection brush. Default `\#333`.\\ -\hspace{1em}brush.border.width & border width of selection brush. Default `1`.\\ -\addlinespace[0.3em] -\multicolumn{2}{l}{\textbf{Tooltip and zoom tools}}\\ -\hspace{1em}tooltip & if show tooltip. Default `TRUE`.\\ -\hspace{1em}zoom & if enable zoom feature. Default `TRUE`.\\ -\bottomrule -\end{longtabu} - -\hyperref[top]{↥ back to top} - -\subsection{\texorpdfstring{ Save chart as -HTML}{ Save chart as HTML}}\label{save-chart-as-html} - -\texttt{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 -\texttt{htmlwidgets::saveWidget} function. - -\begin{Shaded} -\begin{Highlighting}[] -\NormalTok{chart }\OtherTok{\textless{}{-}} \FunctionTok{g3Lollipop}\NormalTok{(mutation.dat,} - \AttributeTok{gene.symbol =} \StringTok{"TP53"}\NormalTok{,} - \AttributeTok{protein.change.col =} \StringTok{"amino\_acid\_change"}\NormalTok{,} - \AttributeTok{plot.options =}\NormalTok{ plot.options)} -\NormalTok{htmlwidgets}\SpecialCharTok{::}\FunctionTok{saveWidget}\NormalTok{(chart, }\StringTok{"g3lollipop\_chart.html"}\NormalTok{)} -\end{Highlighting} -\end{Shaded} - -\hyperref[top]{↥ back to top} - -\section{Session Info}\label{session-info} - -\begin{Shaded} -\begin{Highlighting}[] -\FunctionTok{sessionInfo}\NormalTok{()} -\CommentTok{\#\textgreater{} R version 4.4.0 (2024{-}04{-}24)} -\CommentTok{\#\textgreater{} Platform: x86\_64{-}apple{-}darwin20} -\CommentTok{\#\textgreater{} Running under: macOS Sonoma 14.5} -\CommentTok{\#\textgreater{} } -\CommentTok{\#\textgreater{} Matrix products: default} -\CommentTok{\#\textgreater{} BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib } -\CommentTok{\#\textgreater{} LAPACK: /Library/Frameworks/R.framework/Versions/4.4{-}x86\_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0} -\CommentTok{\#\textgreater{} } -\CommentTok{\#\textgreater{} locale:} -\CommentTok{\#\textgreater{} [1] en\_US.UTF{-}8/en\_US.UTF{-}8/en\_US.UTF{-}8/C/en\_US.UTF{-}8/en\_US.UTF{-}8} -\CommentTok{\#\textgreater{} } -\CommentTok{\#\textgreater{} time zone: America/Los\_Angeles} -\CommentTok{\#\textgreater{} tzcode source: internal} -\CommentTok{\#\textgreater{} } -\CommentTok{\#\textgreater{} attached base packages:} -\CommentTok{\#\textgreater{} [1] stats4 stats graphics grDevices utils datasets methods base } -\CommentTok{\#\textgreater{} } -\CommentTok{\#\textgreater{} other attached packages:} -\CommentTok{\#\textgreater{} [1] g3viz\_1.2.0 kableExtra\_1.4.0 knitr\_1.47 cBioPortalData\_2.16.0 } -\CommentTok{\#\textgreater{} [5] MultiAssayExperiment\_1.30.2 SummarizedExperiment\_1.34.0 Biobase\_2.64.0 GenomicRanges\_1.56.1 } -\CommentTok{\#\textgreater{} [9] GenomeInfoDb\_1.40.1 IRanges\_2.38.0 S4Vectors\_0.42.0 BiocGenerics\_0.50.0 } -\CommentTok{\#\textgreater{} [13] MatrixGenerics\_1.16.0 matrixStats\_1.3.0 AnVIL\_1.16.0 dplyr\_1.1.4 } -\CommentTok{\#\textgreater{} [17] rmarkdown\_2.27 } -\CommentTok{\#\textgreater{} } -\CommentTok{\#\textgreater{} loaded via a namespace (and not attached):} -\CommentTok{\#\textgreater{} [1] rstudioapi\_0.16.0 jsonlite\_1.8.8 magrittr\_2.0.3 GenomicFeatures\_1.56.0 } -\CommentTok{\#\textgreater{} [5] fs\_1.6.4 BiocIO\_1.14.0 zlibbioc\_1.50.0 vctrs\_0.6.5 } -\CommentTok{\#\textgreater{} [9] memoise\_2.0.1 Rsamtools\_2.20.0 RCurl\_1.98{-}1.14 tinytex\_0.51 } -\CommentTok{\#\textgreater{} [13] webshot\_0.5.5 usethis\_2.2.3 htmltools\_0.5.8.1 S4Arrays\_1.4.1 } -\CommentTok{\#\textgreater{} [17] BiocBaseUtils\_1.6.0 lambda.r\_1.2.4 curl\_5.2.1 SparseArray\_1.4.8 } -\CommentTok{\#\textgreater{} [21] sass\_0.4.9 bslib\_0.7.0 desc\_1.4.3 htmlwidgets\_1.6.4 } -\CommentTok{\#\textgreater{} [25] testthat\_3.2.1.1 futile.options\_1.0.1 cachem\_1.1.0 GenomicAlignments\_1.40.0 } -\CommentTok{\#\textgreater{} [29] mime\_0.12 lifecycle\_1.0.4 pkgconfig\_2.0.3 Matrix\_1.7{-}0 } -\CommentTok{\#\textgreater{} [33] R6\_2.5.1 fastmap\_1.2.0 rcmdcheck\_1.4.0 GenomeInfoDbData\_1.2.12 } -\CommentTok{\#\textgreater{} [37] shiny\_1.8.1.1 digest\_0.6.36 colorspace\_2.1{-}0 RaggedExperiment\_1.28.0 } -\CommentTok{\#\textgreater{} [41] ps\_1.7.7 AnnotationDbi\_1.66.0 rprojroot\_2.0.4 pkgload\_1.4.0 } -\CommentTok{\#\textgreater{} [45] RSQLite\_2.3.7 filelock\_1.0.3 RTCGAToolbox\_2.34.0 fansi\_1.0.6 } -\CommentTok{\#\textgreater{} [49] RJSONIO\_1.3{-}1.9 httr\_1.4.7 abind\_1.4{-}5 compiler\_4.4.0 } -\CommentTok{\#\textgreater{} [53] remotes\_2.5.0 withr\_3.0.0 bit64\_4.0.5 BiocParallel\_1.38.0 } -\CommentTok{\#\textgreater{} [57] DBI\_1.2.3 pkgbuild\_1.4.4 highr\_0.11 sessioninfo\_1.2.2 } -\CommentTok{\#\textgreater{} [61] rappdirs\_0.3.3 DelayedArray\_0.30.1 rjson\_0.2.21 tools\_4.4.0 } -\CommentTok{\#\textgreater{} [65] httpuv\_1.6.15 glue\_1.7.0 callr\_3.7.6 restfulr\_0.0.15 } -\CommentTok{\#\textgreater{} [69] promises\_1.3.0 grid\_4.4.0 generics\_0.1.3 tzdb\_0.4.0 } -\CommentTok{\#\textgreater{} [73] tidyr\_1.3.1 data.table\_1.15.4 hms\_1.1.3 xml2\_1.3.6 } -\CommentTok{\#\textgreater{} [77] utf8\_1.2.4 XVector\_0.44.0 pillar\_1.9.0 stringr\_1.5.1 } -\CommentTok{\#\textgreater{} [81] later\_1.3.2 BiocFileCache\_2.12.0 lattice\_0.22{-}6 rtracklayer\_1.64.0 } -\CommentTok{\#\textgreater{} [85] bit\_4.0.5 tidyselect\_1.2.1 Biostrings\_2.72.1 miniUI\_0.1.1.1 } -\CommentTok{\#\textgreater{} [89] svglite\_2.1.3 futile.logger\_1.4.3 xfun\_0.45 brio\_1.1.5 } -\CommentTok{\#\textgreater{} [93] devtools\_2.4.5 DT\_0.33 stringi\_1.8.4 UCSC.utils\_1.0.0 } -\CommentTok{\#\textgreater{} [97] xopen\_1.0.1 yaml\_2.3.8 evaluate\_0.24.0 codetools\_0.2{-}20 } -\CommentTok{\#\textgreater{} [101] tibble\_3.2.1 cli\_3.6.3 systemfonts\_1.1.0 xtable\_1.8{-}4 } -\CommentTok{\#\textgreater{} [105] processx\_3.8.4 roxygen2\_7.3.2 munsell\_0.5.1 jquerylib\_0.1.4 } -\CommentTok{\#\textgreater{} [109] Rcpp\_1.0.12 GenomicDataCommons\_1.28.0 dbplyr\_2.5.0 png\_0.1{-}8 } -\CommentTok{\#\textgreater{} [113] XML\_3.99{-}0.17 rapiclient\_0.1.5 parallel\_4.4.0 ellipsis\_0.3.2 } -\CommentTok{\#\textgreater{} [117] TCGAutils\_1.24.0 readr\_2.1.5 blob\_1.2.4 prettyunits\_1.2.0 } -\CommentTok{\#\textgreater{} [121] profvis\_0.3.8 urlchecker\_1.0.1 bitops\_1.0{-}7 viridisLite\_0.4.2 } -\CommentTok{\#\textgreater{} [125] scales\_1.3.0 purrr\_1.0.2 crayon\_1.5.3 rlang\_1.1.4 } -\CommentTok{\#\textgreater{} [129] KEGGREST\_1.44.1 rvest\_1.0.4 formatR\_1.14} -\end{Highlighting} -\end{Shaded} - -\hyperref[top]{↥ back to top} - -\end{document}