Bi8190 Vizualization of biological data

Faculty of Science
Spring 2010
Extent and Intensity
0/2. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).
Teacher(s)
Mgr. David Zelený, Ph.D. (seminar tutor)
Guaranteed by
Mgr. David Zelený, Ph.D.
Department of Botany and Zoology – Biology Section – Faculty of Science
Contact Person: Mgr. David Zelený, Ph.D.
Timetable
Wed 8:00–9:50 F01B1/709, Wed 8:00–9:50 COMPBR
Prerequisites
The class has two main goals: 1) introduce students to basics and modern trends in vizualization of scientific data (how a figure in good scientific publication should look like, what are the possibilities for visualization different data types, which file formats are the most suitable etc.), and 2) teach them how to produce both simple and more advanced graphs in R software package. The class is rather technically oriented and takes place mostly in front of the computer with running R program, interlaced with theoretical half-hours. Vizualization of biological data is complementary to Bi7920 Analysis of biological data - both courses are focused on work with R program, but while Analysis of biological data is devoted to data analysis, Vizualization focuses on graphical presentation. The class will build on the knowledge learned at Bi5040 Biostatistics - basic course, so student who has already passed this course will be advantaged. Further recommended courses: Bi6549 Methods of phytosociology and Bi7540 Data analysis in community ecology.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The class should teach students how to efectivelly present their data in a graphical form produced by R programme.
Syllabus (in Czech)
  • 1) Základy práce s programem R (formou "simple idiot's guide").
  • 2) Jednoduché grafy (boxploty, histogramy, scatterploty).
  • 3) Barvy - které kombinace nelze použít, jak barvu v Rku namíchat, kdy barvu používat a kdy ne.
  • 4) Formáty obrázků - použít radši jpg, bmp, tiff, nebo snad pdf či eps?
  • 5) Pokročilejší zobrazení dat - trellis diagramy, ordinační diagramy, 3D grafika.
  • 6) Jak vytvořit grafy podle vlastních představ?
Literature
  • MURRELL, Paul. R graphics. Boca Raton: Chapman & Hall/CRC, 2006, xix, 301. ISBN 158488486X. info
  • URL: http://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html
Teaching methods
The class will be held in computer room in Bohunice right in front of the computer - students can directly apply what they learn. During the class there will be 3 homework followed by discussion in next class. Active attending of the class is voluntary, but highly recommended - learning curve of R language is steep and who will miss the train will hardly catch up again. In the end of the class students will individually prepare a small project - graphical visualization of their own or training data. This project will be presented at tha last lesson.
Assessment methods
The last lesson will be held in form of informal "workshop", where will students present results of their graphical work. Students will gain their credit based on their final presentation (and at least two handed homeworks).
Language of instruction
Czech
Further comments (probably available only in Czech)
Study Materials
The course is taught once in two years.
Information on the per-term frequency of the course: v jarním semestru sudých let (2008, 2010, ...).
Information on course enrolment limitations: původně byla kapacita předmětu omezena kapacitou počítačovny v Řečkovicích, po přesunu do Bohunic toto omezení padá
Teacher's information
http://sci.muni.cz/botany/zeleny/vizualizace
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2007, Spring 2008, Spring 2012, spring 2012 - acreditation, Spring 2014, Autumn 2016, Autumn 2018.
  • Enrolment Statistics (Spring 2010, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2010/Bi8190