Difference between revisions of "Lesson08"

From ISSS608-Visual Analytics and Applications
Jump to navigation Jump to search
Line 97: Line 97:
 
* [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.  
 
* [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.  
 
* [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.  
 
* [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.  
 +
 +
==Heatmap==
 +
 +
'''Static heatmap'''
 +
- [https://www.rdocumentation.org/packages/stats/versions/3.6.0/topics/heatmap heatmap()of R stats package.  It draws a simple heatmap.
 +
- [heatmap.2()](https://www.rdocumentation.org/packages/gplots/versions/3.0.1.1/topics/heatmap.2) of **gplots** R package.  It draws an enhanced heatmap compared to the R base function.
 +
- [pheatmap()](https://www.rdocumentation.org/packages/pheatmap/versions/1.0.12/topics/pheatmap) of [**pheatmap**](https://www.rdocumentation.org/packages/pheatmap/versions/1.0.12) 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**](https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html) 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**](https://cran.r-project.org/web/packages/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](https://rlbarter.github.io/superheat/).
 +
  
 
==Treemaps==
 
==Treemaps==

Revision as of 23:09, 8 March 2020

Vaa logo.jpg ISSS608 Visual Analytics and Applications

About

Weekly Session

Assignment

Visual Analytics Project

Course Resources

 


Visualising and Analysing High-dimensional 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 - [https://www.rdocumentation.org/packages/stats/versions/3.6.0/topics/heatmap heatmap()of R stats package. It draws a simple heatmap. - [heatmap.2()](https://www.rdocumentation.org/packages/gplots/versions/3.0.1.1/topics/heatmap.2) of **gplots** R package. It draws an enhanced heatmap compared to the R base function. - [pheatmap()](https://www.rdocumentation.org/packages/pheatmap/versions/1.0.12/topics/pheatmap) of [**pheatmap**](https://www.rdocumentation.org/packages/pheatmap/versions/1.0.12) 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**](https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html) 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**](https://cran.r-project.org/web/packages/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](https://rlbarter.github.io/superheat/).


Treemaps

Sunburst Diagram

Retrieved from ‘https://wiki.smu.edu.sg/1920t2isss608/index.php?title=Lesson08&oldid=1434’