Posted  by  admin

Gplots Color

Release 2.17.0 - 2015-05-01

Color

Ggplot2 Color Numerical

# gplots contains the heatmap.2 function library. Max = 1), nrow = 50) # following code limits the lowest and highest color to 5%, and 95% of your range.

  1. Gplots: Various R Programming Tools for Plotting Data. Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary.
  2. In gplots: Various R Programming Tools for Plotting Data. Description Usage Arguments Details Value Author(s) See Also Examples. View source: R/colorpanel.R. Colorpanel generate a set of colors that varies smoothly.redgreen, greenred, bluered, and redblue generate red-black-green, green-black-red, red-white-blue, and blue-white-red colorbars, respectively.

New Features:

  • heatmap.2() has two new arguments, ‘colRow’ and ‘colCol’ to control the color of row and column text labels. See the man page for examples.

  • heatmap.2() has been modified to make it easier to extract and plot subclusters from a large heatmap. Simply pass the dendrogram of the subcluster together with the full data matrix and, optionally, the breaks of the full heatmap in order to obtain the same color scaling. (Suggestion and patch contributed by Ilia Kats.)

  • venn() now returns a list of the members of each set intersection in the attribute ‘intersections’. This can be disabled using the argument ‘intersection=FALSE’ (Patch by Steffen Möller.)

Bug Fixes:

  • In heatmap.2(), the color key now properly handles color breaks that are not equally spaced. (Issue reported by Tim Richter-Heitmann.)

  • In heatmap.2(), row/column traces in could be plotted on the wrong row/column.

  • plotCI() now properly respects the ‘type=’ argument. (Bug report and correction by Wiktor Żelazny.)

  • Remove stray browser() call from overplot()

  • In the balloonplot() examples, explicitly specify the ‘neworder’ argument to gplots:::reorder.factor to prevent errors.

Other Changes:

  • smartlegend() is now deprecated because the relative positioning feature (‘top’, ‘right’) has been added to graphics::legend(). Calling smartlegend() will generate a warning.

  • boxplot.n() and plot.lm2() are defunct have been removed. Use of these functions will now generate an error.

  • Update out-of-date URLs in man pages.

This data visualization example include:
* Hierarchical clustering, dendrogram and heat map based on normalized odds ratios
* The dendrogram was built separately to give color to dendrogram’s branches/labels based on cluster using dendextend
* Heatmap is made by heatmap.2 from gplots using the built dendrogram
* The rows are sorted by means from highest to lowest, it can be done in either the dendrogram or the heatmap.2
* Use color palettes from colorspace

Data

Gplots Venn

  • YRBSS (Youth Risk Behavior Surveillance System) survey data from CDC. This example plots the odds ratios of 63 behavioral questions on one question regarding disordered eating.
  • The odds ratios are median centered by column and log2 transformed
Color

Version 2: color only the labels.

  • There is no need to use the predesigned dend1 in heatmap.2
  • But then need to reorder the trees by adding reorderfun
  • Still need to create the col_labels

Version 3: If there is no color, and we do not reorder the branches

  • Then there is no need to create an extra dendrogram using dendextend

Gplots Heatmap.2 Colors

Please enable JavaScript to view the comments powered by Disqus.