Difference between revisions of "Lesson08"

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<font size="5">'''Visualising and Analysing High-dimensional Data '''</font>
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<font size="5">'''Visualising and Analysing Multidimensional Data '''</font>
  
 
=Content=
 
=Content=
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=R Packages=
 
=R Packages=
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==Correlation Matrix==
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* [https://ggobi.github.io/ggally/#ggallyggscatmat ggscatmat] and [https://ggobi.github.io/ggally/#ggallyggpairs ggpairs] of [https://ggobi.github.io/ggally/index.html GGally]
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* [https://cran.r-project.org/web/packages/corrplot/index.html corrplot]. A graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. In addition, corrplot is good at details, including choosing color, text labels, color labels, layout, etc.
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* [https://cran.r-project.org/web/packages/corrgram/index.html corrgram] calculates correlation of variables and displays the results graphically. Included panel functions can display points, shading, ellipses, and correlation values with confidence intervals.
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==Heatmap==
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'''Static heatmap'''
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* [https://www.rdocumentation.org/packages/stats/versions/3.6.0/topics/heatmap heatmap()] of R stats package.  It draws a simple heatmap.
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* [https://www.rdocumentation.org/packages/gplots/versions/3.0.1.1/topics/heatmap.2 heatmap.2()] of **gplots** R package.  It draws an enhanced heatmap compared to the R base function.
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* [https://www.rdocumentation.org/packages/pheatmap/versions/1.0.12/topics/pheatmap pheatmap()] of [https://www.rdocumentation.org/packages/pheatmap **pheatmap**] R package.  **pheatmap** package also known as Pretty Heatmap.  The package provides functions to draws pretty heatmaps and provides more control to change the appearance of heatmaps.
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* [https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html **ComplexHeatmap**] package of R/Bioconductor package.  The package draws, annotates and arranges complex heatmaps (very useful for genomic data analysis).  The full reference guide of the package is available [here](https://jokergoo.github.io/ComplexHeatmap-reference/book/).
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* [https://cran.r-project.org/web/packages/superheat/ **superheat**] package: A Graphical Tool for Exploring Complex Datasets Using Heatmaps.  A system for generating extendable and customizable heatmaps for exploring complex datasets, including big data and data with multiple data types.  The full reference guide of the package is available [https://rlbarter.github.io/superheat/ here].
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'''Interactive Heatmap'''
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* [https://cran.r-project.org/web/packages/heatmaply/index.html heatmaply:] Make Interactive Cluster Heat Maps Using 'plotly'
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* [https://cran.r-project.org/web/packages/d3heatmap/index.html d3heatmap d3heatmap:] Make Interactive Heat Maps Using 'htmlwidgets' and 'D3.js.
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* [https://cran.r-project.org/web/packages/iheatmapr/index.html iheatmapr:] Make complex, interactive heatmaps. Detail information are available at [https://docs.ropensci.org/iheatmapr/ here].
  
 
==Treemaps==
 
==Treemaps==
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==Sunburst Diagram==
 
==Sunburst Diagram==
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** [https://cran.r-project.org/web/packages/sunburstR/ sunburstR]
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* [https://cran.r-project.org/web/packages/sunburstR/ sunburstR]
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** [https://cran.r-project.org/web/packages/sunburstR/vignettes/sunburst-2-0-0.html Sunburst 2.0.0]
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* [https://cran.r-project.org/web/packages/sunburstR/vignettes/sunburst-2-0-0.html Sunburst 2.0.0]
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** [http://timelyportfolio.github.io/sunburstR/example_baseball.html Visualize Baseball with sunburstR]
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* [http://timelyportfolio.github.io/sunburstR/example_baseball.html Visualize Baseball with sunburstR]
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** [https://medium.com/optima-blog/create-basic-sunburst-graphs-with-ggplot2-7d7484d92c61 Create Basic Sunburst Graphs with ggplot2]
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* [https://medium.com/optima-blog/create-basic-sunburst-graphs-with-ggplot2-7d7484d92c61 Create Basic Sunburst Graphs with ggplot2]
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** [https://cran.r-project.org/web/packages/circlize/index.html circlize: circular visualization in R]
 
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** [https://jokergoo.github.io/circlize_book/book/ Circular Visualization in R]
 

Latest revision as of 08:20, 9 March 2020

Vaa logo.jpg ISSS608 Visual Analytics and Applications

About

Weekly Session

Assignment

Visual Analytics Project

Course Resources

 


Visualising and Analysing Multidimensional Data

Content

  • Introduction to High-dimensional Data
  • Bivariate Matrix
    • Trellis
    • Correlation Matrix
    • Correlogram
  • Multivariate Data Visualisation
    • Ternary Plot
    • Glyphs or Star Plot
    • Heatmap
    • Parallel Coordinate Plot
  • Space-constrained visualization of hierarchies
    • Treemaps
    • Sunburst diagram


Readings

Core Readings

Multivariate Methods

Treemaps


Optional Readings

Multivariate Methods

Treemaps

R Packages

Correlation Matrix

  • ggscatmat and ggpairs of GGally
  • corrplot. A graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. In addition, corrplot is good at details, including choosing color, text labels, color labels, layout, etc.
  • corrgram calculates correlation of variables and displays the results graphically. Included panel functions can display points, shading, ellipses, and correlation values with confidence intervals.

Heatmap

Static heatmap

  • heatmap() of R stats package. It draws a simple heatmap.
  • heatmap.2() of **gplots** R package. It draws an enhanced heatmap compared to the R base function.
  • pheatmap() of **pheatmap** R package. **pheatmap** package also known as Pretty Heatmap. The package provides functions to draws pretty heatmaps and provides more control to change the appearance of heatmaps.
  • **ComplexHeatmap** package of R/Bioconductor package. The package draws, annotates and arranges complex heatmaps (very useful for genomic data analysis). The full reference guide of the package is available [here](https://jokergoo.github.io/ComplexHeatmap-reference/book/).
  • **superheat** package: A Graphical Tool for Exploring Complex Datasets Using Heatmaps. A system for generating extendable and customizable heatmaps for exploring complex datasets, including big data and data with multiple data types. The full reference guide of the package is available here.

Interactive Heatmap

  • heatmaply: Make Interactive Cluster Heat Maps Using 'plotly'
  • d3heatmap d3heatmap: Make Interactive Heat Maps Using 'htmlwidgets' and 'D3.js.
  • iheatmapr: Make complex, interactive heatmaps. Detail information are available at here.

Treemaps

Sunburst Diagram

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