Corn drawing

HOME

People

Publications/ Presentations

Traits

Germplasm

Field Program

R code

Visiting

Program History

Links

Site

R code and Data Analysis

Through research, teaching (AGRO 643) and making figures for presentations we have developed extensive R code. Most of this is not user friendly but hopefully others can benefit from it. Note you will need R and probably some experience to run these. Please acknowledge the source if you find these useful.

 

 

1. Plotting Texas County Data

Texas County Data

Instead of filling in each county with a color manually - a spreadsheet with values can be used. You will need to download the maps package within R [Packages --> Install Package(s)]. The spreadsheet has multiple columns of data which you can select to plot.
THREE FILES ARE NEEDED
1. CODE - You must change the file path (in red) you can change the column of data plotted (in blue).
2. DATA - downloaded freely from the USDA-NASS but saved as a tab delimited text file
3. COUNTY NAMES - also modified from the USDA-RMA


A nice tool to make sure this is plotting correctly is the Texas County Locator.

 

2. Plotting QTL for Many Traits

The code used to produce the QTL mapping figure used in a few crop science publications:

1. ReadMe (rich text)
2. GraphQTLinR (rich text)
3. GeneticMap (.txt - using the map from Murray et al. 2008a as an example.)
4. QTLr (.txt - using the QTL from Murray et al. 2008a as an example.)
Mayfield QTL

Mayfield, K. L., S. C. Murray*, W. L. Rooney, T. Isakeit, and G. A. Odvody. 2011. Confirmation of QTL Reducing Aflatoxin in Maize Testcrosses. Crop Science. doi: 10.2135/cropsci2011.02.0112

Murray, S.C., A.Sharma, W.L. Rooney, P.E. Klein PE, J.E. Mullet, S.E. Mitchell, and S. Kresovich*. 2008a. Genetic improvement of sorghum as a biofuel feedstock I: quantitative loci for stem sugar and grain nonstructural carbohydrates. Crop Science 48:2165-2179.

Murray, S.C., A.Sharma, W.L. Rooney, P.E. Klein PE, J.E. Mullet, S.E. Mitchell, and S. Kresovich*. 2008b. Genetic improvement of sorghum as a biofuel feedstock II: quantitative loci for stem and leaf structural carbohydrates. Crop Science 48:2180-2193.

 

3. Make a Heat Map of Field Variation

Allows visualization of areas of the field with more or less variation.

 

 

 

 

Texas A&M University LogoAgrilife Research Logo