Practical Bioinformatics for Life Scientists

Week 13, Lecture 26

István Albert

Bioinformatics Consulting CenterPenn State

Visualizing high dimensionality data

by Hadley Wickham: http://had.co.nz/

There is nothing like it in any programming environment!

Parts of this presentation follow the tutorial of ggplot2

Getting started with ggplot2

http://had.co.nz/ggplot2/book/qplot.pdf

We will start out with example plots from this manual

Then at the end wegenerate a peak distribution plotaround gene starts sites.

Install ggplot2

diamonds.txt (data comes with ggplot2)

NOTEFor the next few slidesI will be changing only

line 10

(sometimes we use alldata or just the small

data)

ggplot2 concepts

• geometry what plot looks like

• faceting how many plots/panels

• statistics transformation on the data

• positioning fine tunes locations in the plot

• scales maps data to an x,y coordinate

Faceting - multiplots

Faceting and shapes and colors

scripts are in supporting data located in the 26.tar.gz file on the website

Recall intersecting peaks with genes from the Chip-Seq lecture. We needan R script to prepare the data for plotting. Code included in this week’s download

Homework 26

Generate four plots with ggplot2 that demonstrate one ore more features including:

– histograms

– shapes

– colors

– faceting