a grammar of graphics for genomics
play

A Grammar of Graphics for Genomics The ggbio Package Michael - PowerPoint PPT Presentation

Jun 02, 2023 •142 likes •809 views

A Grammar of Graphics for Genomics The ggbio Package Michael Lawrence Genentech August 29, 2012 Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 1 / 18 Outline 1 Motivation 2 High-level Plots 3 Grammar

  1. A Grammar of Graphics for Genomics The ggbio Package Michael Lawrence Genentech August 29, 2012 Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 1 / 18

  2. Outline 1 Motivation 2 High-level Plots 3 Grammar Components Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 2 / 18

  3. Outline 1 Motivation 2 High-level Plots 3 Grammar Components Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 3 / 18

  4. Data on the Genome • Comes in two flavors: • Annotations (genes, TF binding sites, ...) • Experimental measurements (sequence reads) • Both types are tied to genomic coordinates, providing a common axis that permits cross-dataset comparison and inference • Typically stored as a table, with the range as a fundamental variable type, plus metadata Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 4 / 18

  5. Data on the Genome • Comes in two flavors: • Annotations (genes, TF binding sites, ...) • Experimental measurements (sequence reads) • Both types are tied to genomic coordinates, providing a common axis that permits cross-dataset comparison and inference • Typically stored as a table, with the range as a fundamental variable type, plus metadata 120.928 Mb 120.93 Mb 120.932 Mb 120.934 Mb 120.936 Mb 120.938 Mb Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 4 / 18

  6. Data on the Genome • Comes in two flavors: • Annotations (genes, TF binding sites, ...) • Experimental measurements (sequence reads) • Both types are tied to genomic coordinates, providing a common axis that permits cross-dataset comparison and inference • Typically stored as a table, with the range as a fundamental variable type, plus metadata 60 50 40 30 20 10 0 120928000 120930000 120932000 120934000 120936000 120938000 Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 4 / 18

  7. Data on the Genome • Comes in two flavors: • Annotations (genes, TF binding sites, ...) • Experimental measurements (sequence reads) • Both types are tied to genomic coordinates, providing a common axis that permits cross-dataset comparison and inference • Typically stored as a table, with the range as a fundamental variable type, plus metadata 60 50 40 30 20 10 0 120.928 Mb 120.93 Mb 120.932 Mb 120.934 Mb 120.936 Mb 120.938 Mb Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 4 / 18

  8. Data on the Genome • Comes in two flavors: • Annotations (genes, TF binding sites, ...) • Experimental measurements (sequence reads) • Both types are tied to genomic coordinates, providing a common axis that permits cross-dataset comparison and inference • Typically stored as a table, with the range as a fundamental variable type, plus metadata seqnames start end strand exon id tx id 10 120927215 120928045 - 129230 14886,14887 10 120928689 120928854 - 129229 14886,14887 10 120931894 120931997 - 129228 14886,14887 10 120933249 120933384 - 129227 14886,14887 10 120933963 120934069 - 129226 14886 10 120933963 120934104 - 119757 14887 10 120936533 120936665 - 119756 14887 10 120936552 120936665 - 129225 14886 10 120938267 120938345 - 129224 14886,14887 Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 4 / 18

  9. Challenges Big data, wide spaces • Need summaries that are efficiently computed, communicate more with less and expose the most interesting aspects of the data • Need different ways of viewing the data, depending on the density and scale, from whole genome to single basepair Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 5 / 18

  10. Challenges Big data, wide spaces 120.928 Mb 120.93 Mb 120.932 Mb 120.934 Mb 120.936 Mb 120.938 Mb • Need summaries that are efficiently computed, communicate more with less and expose the most interesting aspects of the data • Need different ways of viewing the data, depending on the density and scale, from whole genome to single basepair Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 5 / 18

  11. Challenges Big data, wide spaces 60 50 40 30 20 10 0 120.928 Mb 120.93 Mb 120.932 Mb 120.934 Mb 120.936 Mb 120.938 Mb • Need summaries that are efficiently computed, communicate more with less and expose the most interesting aspects of the data • Need different ways of viewing the data, depending on the density and scale, from whole genome to single basepair Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 5 / 18

  12. Challenges Big data, wide spaces 300000 250000 200000 150000 100000 50000 0 0 Mb 50 Mb 100 Mb • Need summaries that are efficiently computed, communicate more with less and expose the most interesting aspects of the data • Need different ways of viewing the data, depending on the density and scale, from whole genome to single basepair Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 5 / 18

  13. Existing Tools UCSC IGB IGV Circos GViz Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 6 / 18

  14. Existing Tools UCSC IGB IGV Circos GViz Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 6 / 18

  15. Existing Tools UCSC IGB IGV Circos GViz Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 6 / 18

  16. Existing Tools UCSC IGB IGV Circos GViz Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 6 / 18

  17. Existing Tools UCSC IGB IGV Circos GViz Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 6 / 18

  18. Existing Tools UCSC IGB IGV Circos GViz Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 6 / 18

  19. Existing Tools UCSC IGB IGV Circos GViz Limitations • Limited to one type of view (linear or circular) • Not tightly integrated with an analysis environment through standard, abstract data structures (except GViz) • No low-level toolkit for prototyping new types of graphics Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 6 / 18

  20. Grammars of Graphics • A grammar of graphics is a language for expressing plots • Graphics are constructed through the combination of various types of primitives; like legos for graphics • The most prominent grammar was introduced by Wilkinson’s book The Grammar of Graphics • Wilkinson’s grammar was extended by Wickham and the ggplot2 package Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 7 / 18

  21. Grammars of Graphics • A grammar of graphics is a language for expressing plots • Graphics are constructed through the combination of various types of primitives; like legos for graphics • The most prominent grammar was introduced by Wilkinson’s book The Grammar of Graphics • Wilkinson’s grammar was extended by Wickham and the ggplot2 package Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 7 / 18

  22. Grammars of Graphics • A grammar of graphics is a language for expressing plots • Graphics are constructed through the combination of various types of primitives; like legos for graphics • The most prominent grammar was introduced by Wilkinson’s book The Grammar of Graphics • Wilkinson’s grammar was extended by Wickham and the ggplot2 package Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 7 / 18

  23. Grammars of Graphics • A grammar of graphics is a language for expressing plots • Graphics are constructed through the combination of various types of primitives; like legos for graphics • The most prominent grammar was introduced by Wilkinson’s book The Grammar of Graphics • Wilkinson’s grammar was extended by Wickham and the ggplot2 package Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 7 / 18

  24. The ggbio Package • An R/Bioconductor package that extends the Wilkinson/Wickham grammar for applications in genomics • Integrated with Bioconductor • Operates on standard, abstract genomic data structures • Leverages efficient range-based algorithms • Programming interface has two levels of abstraction: autoplot Maps Bioconductor data structures to plots grammar Mix and match to create custom plots Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 8 / 18

  25. Outline 1 Motivation 2 High-level Plots 3 Grammar Components Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 9 / 18

  26. Basic Plots Gene Structures Read Alignments Sequence Multiple Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 10 / 18

  27. Basic Plots Gene Structures Read Alignments Sequence Multiple 120.928 Mb 120.93 Mb 120.932 Mb 120.934 Mb 120.936 Mb 120.938 Mb Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 10 / 18

  28. Basic Plots Gene Structures Read Alignments Sequence Multiple 60 50 40 30 20 10 0 120928000 120930000 120932000 120934000 120936000 120938000 Michael Lawrence (Genentech) A Grammar of Graphics for Genomics August 29, 2012 10 / 18

Recommend

Workshop 5.2: The Grammar of Graphics Murray Logan 16 Jul 2017 Section 1 Graphics in R

Workshop 5.2: The Grammar of Graphics Murray Logan 16 Jul 2017 Section 1 Graphics in R

Workshop 5.2: The Grammar of Graphics Murray Logan 16 Jul 2017 Section 1 Graphics in R Options Traditional (base) graphics isolated instructions to the device Grid graphics instruction sets lattice ggplot2 > library

1.53k views • 88 slides
Show the Right Numbers ggplot IMPLEMENTS A GRAMMAR OF GRAPHICS The grammar is a set of rules

Show the Right Numbers ggplot IMPLEMENTS A GRAMMAR OF GRAPHICS The grammar is a set of rules

Show the Right Numbers ggplot IMPLEMENTS A GRAMMAR OF GRAPHICS The grammar is a set of rules for how produce graphics from data, taking pieces of data and mapping them to geometric objects (like points and lines) that have aesthetic attributes

1.75k views • 171 slides
Introduction to Data Science: Basic Let's create a dot plot of the example points and text, by

Introduction to Data Science: Basic Let's create a dot plot of the example points and text, by

Data Visualization Grammar of Graphics (ggplot) Boxplot Histogram Bar graph Scatter plot Frequently Used Plots Plot Construction Details Plot Construction Details Grammar of Graphics (ggplot) Grammar of Graphics (ggplot) Grammar of

644 views • 15 slides
Genomics Genomics extravaganza extravaganza Genomics Genomics overview overview Genomics

Genomics Genomics extravaganza extravaganza Genomics Genomics overview overview Genomics

A Genomics Genomics extravaganza extravaganza Genomics Genomics overview overview Genomics analysis of the structure and function of very large numbers of genes (often the entire genome) undertaken in a simultaneous fashion.

632 views • 37 slides
Workshop 5.2: The Grammar of Graphics Murray Logan July 16, 2017 Table of contents 1

Workshop 5.2: The Grammar of Graphics Murray Logan July 16, 2017 Table of contents 1

-1- Workshop 5.2: The Grammar of Graphics Murray Logan July 16, 2017 Table of contents 1 Graphics in R 1 2 Layers 5 3 Primary geometric objects 9 4 Secondary geometric objects 20 5 Coordinate systems 22 6 Scales 24 7

692 views • 40 slides
Genomics extravaganza Genomics overview Genomics analysis of the structure and function of very

Genomics extravaganza Genomics overview Genomics analysis of the structure and function of very

A Genomics extravaganza Genomics overview Genomics analysis of the structure and function of very large numbers of genes (often the entire genome) undertaken in a simultaneous fashion. Structural genomics includes the genetic mapping,

811 views • 37 slides
Graphics Murray Cole Graphics 1 Graphics 2 Graphics 3 Graphics 4 Graphics 5 Graphics 6

Graphics Murray Cole Graphics 1 Graphics 2 Graphics 3 Graphics 4 Graphics 5 Graphics 6

I V N E U R S E I H T Y T O H F G R E U D I B N Graphics Murray Cole Graphics 1 Graphics 2 Graphics 3 Graphics 4 Graphics 5 Graphics 6 class Smiley extends JFrame { public Smiley() { super ("Love n

638 views • 24 slides
VISUALISING DATA IN R OU24 Graduate Skills Class Damon Wischik Rs Grammar of Graphics

VISUALISING DATA IN R OU24 Graduate Skills Class Damon Wischik Rs Grammar of Graphics

VISUALISING DATA IN R OU24 Graduate Skills Class Damon Wischik Rs Grammar of Graphics codifies some standard patterns in plotting data. It will simplify your life if you learn the way it thinks, and if you dont step outside its scope.

992 views • 40 slides
ggplot and the GRAMMAR OF GRAPHICS MAPPING vs SETTING AESTHETICS p <- ggplot (data =

ggplot and the GRAMMAR OF GRAPHICS MAPPING vs SETTING AESTHETICS p <- ggplot (data =

ggplot and the GRAMMAR OF GRAPHICS MAPPING vs SETTING AESTHETICS p <- ggplot (data = gapminder, mapping = aes (x = gdpPercap, y = lifeExp, color = "purple")) p + geom_point () + geom_smooth (method = "loess") +

491 views • 31 slides
High throughput methods approches in genomics D. Puthier Genomics The science for the 21st

High throughput methods approches in genomics D. Puthier Genomics The science for the 21st

High throughput methods approches in genomics D. Puthier Genomics The science for the 21st century Ewan Birney(EMBL-EBI) at GoogleTech talk Genomics Genomics is the discipline which aims at studying genome (structure, function of

802 views • 59 slides
CS378 - Mobile Computing 3D Graphics 2D Graphics android.graphics library for 2D graphics

CS378 - Mobile Computing 3D Graphics 2D Graphics android.graphics library for 2D graphics

CS378 - Mobile Computing 3D Graphics 2D Graphics android.graphics library for 2D graphics (not Java AWT and Swing) classes such as Canvas, Drawable, Bitmap, and others to create 2D graphics Various attempts to make two d graphics

411 views • 40 slides
Introduction to English Linguistics 4: Grammar and Syntax I Grammar and Syntax Grammar The

Introduction to English Linguistics 4: Grammar and Syntax I Grammar and Syntax Grammar The

Introduction to English Linguistics 4: Grammar and Syntax I Grammar and Syntax Grammar The rules of language, comprising syntax and inflectional morphology Syntax The hierarchical structure of language Lexical Words (Open Class) Noun

539 views • 31 slides
Outline Part 1 Introduction to Genomics Part 2 Visual Design for Genomics Part 3 Hands-On

Outline Part 1 Introduction to Genomics Part 2 Visual Design for Genomics Part 3 Hands-On

Visual Analytics for Genomics Cydney Nielsen ! BC Cancer Agency ! Vancouver, BC, Canada ! Outline Part 1 Introduction to Genomics Part 2 Visual Design for Genomics Part 3 Hands-On Design Exercise Part 1 Introduction to Genomics Genomics

757 views • 71 slides
Introduction to English Linguistics 4: Grammar and Syntax Grammar and Syntax Grammar The rules

Introduction to English Linguistics 4: Grammar and Syntax Grammar and Syntax Grammar The rules

Introduction to English Linguistics 4: Grammar and Syntax Grammar and Syntax Grammar The rules of language, comprising syntax and inflection Syntax The hierarchical structure of language Lexical Words, Open Class Noun Adjective

739 views • 39 slides
GRAMMAR THROUGH HUMOR BRANDY SHOOKS & WHITNEY SCHARER TEACHING GRAMMAR THROUGH HUMOR Having

GRAMMAR THROUGH HUMOR BRANDY SHOOKS & WHITNEY SCHARER TEACHING GRAMMAR THROUGH HUMOR Having

TEACHING GRAMMAR THROUGH HUMOR BRANDY SHOOKS & WHITNEY SCHARER TEACHING GRAMMAR THROUGH HUMOR Having difficulty getting your students interested and excited about grammar? Participants in this session will gain tools to present grammar in

675 views • 28 slides
Combinatory Categorial Grammar The effort to develop natural language grammars and

Combinatory Categorial Grammar The effort to develop natural language grammars and

Combinatory Categorial Grammar Goal Mildly-context sensitive grammar framework, with provable polynomial parseability To present the intuitions behind Combinatory Categorial Grammar as a framework for relating the structure of a linguistic

280 views • 13 slides
Comparative Genomics Comparative Genomics Common Themes Gene and functional pathway

Comparative Genomics Comparative Genomics Common Themes Gene and functional pathway

Comparative Genomics Comparative Genomics Common Themes Gene and functional pathway presence/absence Identification, alignment of orthologs Structural analysis and comparison Comparative Genomics Basic Local Alignment Search Tool

480 views • 14 slides
clinical genomics Melbourne Genomics Health Alliance Melbourne Genomics Health Alliance Medical

clinical genomics Melbourne Genomics Health Alliance Melbourne Genomics Health Alliance Medical

Digital tools to enable clinical genomics Melbourne Genomics Health Alliance Melbourne Genomics Health Alliance Medical Medical Scientist Masters of Genetic Clinical Health service Workforce Variant Curator Genetic Trainee Clinician CPD

680 views • 23 slides
Grammar A grammar consists of the following: CS 3813: Introduction to Formal a set of

Grammar A grammar consists of the following: CS 3813: Introduction to Formal a set of

Grammar A grammar consists of the following: CS 3813: Introduction to Formal a set of terminals (same as an alphabet) Languages and Automata a set NT of nonterminal symbols, including a starting symbol S NT a set R of

426 views • 4 slides
Grammar Formalisms: C-structures are represented with trees. Lexical Functional Grammar (LFG)

Grammar Formalisms: C-structures are represented with trees. Lexical Functional Grammar (LFG)

Kallmeyer/Lichte/Maier Grammar Formalisms Kallmeyer/Lichte/Maier Grammar Formalisms Principle ideas of LFG (1) Lexical Functional Grammar (Kaplan & Bresnan, 1982): One level of constituent structure, c-structure, non-transformational.

524 views • 6 slides
WHAT DO YOU WANT TO TEACH GRAMMAR OR ENGLISH? Seven bad reasons for teaching grammar

WHAT DO YOU WANT TO TEACH GRAMMAR OR ENGLISH? Seven bad reasons for teaching grammar

WHAT DO YOU WANT TO TEACH GRAMMAR OR ENGLISH? Seven bad reasons for teaching grammar Because it s there. Because it s tidy. Because I can test it. Because it makes people feel secure. Because it formed my character.

532 views • 36 slides
Graphics Processing CS418 Computer Graphics John C. Hart Graphics Processing Graphics

Graphics Processing CS418 Computer Graphics John C. Hart Graphics Processing Graphics

Graphics Processing CS418 Computer Graphics John C. Hart Graphics Processing Graphics Processor Triangle mesh with Image of RGB-colored vertices at 3-D floating- pixels at 2-D integer point spatial coordinate planar coordinate positions

542 views • 14 slides
Mapping Data to Graphics Session 3 PMAP 8921: Data Visualization with R Andrew Young School of

Mapping Data to Graphics Session 3 PMAP 8921: Data Visualization with R Andrew Young School of

Mapping Data to Graphics Session 3 PMAP 8921: Data Visualization with R Andrew Young School of Policy Studies May 2020 1 / 67 Plan for today Data, aesthetics, & the grammar of graphics Grammatical layers Aesthetics in extra dimensions

937 views • 67 slides
Comparative Genomics: Comparative Genomics: Sequence, Structure, Sequence, Structure, and

Comparative Genomics: Comparative Genomics: Sequence, Structure, Sequence, Structure, and

Comparative Genomics: Comparative Genomics: Sequence, Structure, Sequence, Structure, and Networks and Networks Bonnie Berger MIT Comparative Genomics Comparative Genomics Look at the same kind of data across species with the hope that

1.06k views • 59 slides

More recommend