Generate Comparison Plot Reports

library(qgert)

Disclaimer

The definition of a comparison plot report and how such reports are generated is described in this vignette.

Terminology

A comparison plot report is a document that shows a series of comparison plots arranged in two columns from two subsequent routine evaluations. Please have a look at the separate article on comparison plots to find how these plots are defined an how they are produced.

Comparison Plot Report

Comparison plot reports can come in two different forms. The first is a generic form and the second is specific for routine genetic evaluations.

Generic Form

The generic form of the comparison plot report requires two directories with a corresponding set of plots or diagrams. The diagrams must be available in .pdf or .png format. The correspondence between a pair of plots is established via the name of the plot file. Corresponding plots are shown side-by-side in the comparison plot report.

Routine Genetic Evaluations

Comparison plots are done during each routine evaluation for every block of traits. These plots by themselves are only meaningful with a lot of expertise and experience. But when comparing the same plot to the version that was produced during the previous evaluation, then the quality of the plot can be assessed qualitatively in the sense that it is possible to say, whether the characteristics of the current evaluation represented by a specific comparison plot are better compared to the same characteristics from the previous evaluation.

As a consequence of that the comparison of two plots of the same characteristics from two subsequent routine evaluations provides important information. Therefore the arrangement of two plots of the same characteristics from two subsequent routine evaluations next to each other in two columns makes the comparison seamless and efficient.

Example

Comparison plot reports can either be generated by calling the R-wrapper function for each trait group. Using the fertility trait group as an example, the abbreviation is fbk and the corresponding R wrapper function is

qgert::create_ge_compare_plot_report_fbk(pn_cur_ge_label = 1912, pn_prev_ge_label = 1908)

The above function call creates the comparison plot reports for trait group fbk.

The same comparison plot report can be genrated using the shell script called create_comp_plot_report_fbk.sh. After changing to the evaluation directory, the call to the shell script shown below produces the comparison plot report.

cd /qualstorzws01/data_zws/fbk
./prog/create_comp_plot_report_fbk.sh -c 1912 -p 1908

For trait groups other than fbk there are analogous R wrapper functions and corresponding bash scripts.

Updates

Whenever a new version of the comparison plot report creation pipeline is released, two steps must be performed.

1. Update the R-package qgert using devtools::install_github("fbzwsqualitasag/qgert") and
2. Updating the bash scripts using the following statement

cd /qualstorzws01/data_zws/fbk
/home/zws/lib/R/library/qgert/bash/install_script.sh -s /home/zws/lib/R/library/qgert/bash/create_comp_plot_report_fbk.sh -t prog

The above statement updates the bash script create_comp_plot_report_fbk.sh in subdirectory prog for the trait group fbk.