R-Code to evaluate Drosophila Time Series data. DTSevaluation is an evaluation R-code to analyze, visualize and statistically evaluate Drosophila Time Series data.
| R Files | Description |
|---|---|
| evaluate_project.R | R-script reads the YAML DTS project file and analyses, visualizes and statistically evaluates the DTS data. The output is amalgamated into individual data files for each fly as well as a comprehensive HTML output file for the entire project. |
| evaluate_xml_file.R | Single fly data evaluation script. Evaluates each file separately and visualizes this as an HTML output. |
| include | Subfolder containing routines and code required for data loading and anylsis. Contains install.R for installation of dependencies. |
| example_data | Subfolder containing examledata with YAML files and HTML report sheets. |
| DTS_plotfunctions.R | Contains all the plotting functions for DTS data. |
| Data Files | Description |
|---|---|
| <project_file>.yml | The project YAML file contains exclusively meta-data containing grouping-information which links each individual datafile to a project |
| <data_file>.xml | The xml file contains all the necessary meta-data for that particular fly: name of the experimenter, genotype, FlyBaseID, fly identifier(name), the experimental sequence descriptiond as well as the time series data (raw data). The xml file is generated by the software running the DTS experiment. |
The following instructions is a brief explanation on how to use the DTS evaluation script. For a more detailed description see the Drosophila Time Series Data Model.
- R-script files (evaluate_project.Rmd, evaluate_xml_file.R) need to be in the same directory.
- Datafiles must be within the same folder as the Project YAML file, but ideally not in the same folder as the R-script files.
The project file contain all the meta-data for the particular experiment/project. It contains grouping information that links each experimental fly/file to a particular project. In addition to this it also contains information about the project such as a description and experimental comments. For each project, the YAML file needs to be updated with the necessary user information:
- Author: Information about the experimenter.
- Resources: The list of files for each experimental group, between 1 and 3 groups. Each datafile (with .xml file extension) needs to be listed under the "data" heading in resources. In addition to the filelist the user also needs to provide name, title and description of each experimental group. Name and title is free-text descriptions whereas description is categorical and limited to the following: Ctrl/Control, Experimental/Test/Exp (depending on if that particular group is experimental or a control group)
- The statistical evaluation is determined in the "data" heading in single.group, two.groups and three.groups. The data is binary where 1 corresponds to "yes" and 0 to "no". See example file or The Drosophila Time Series Data Model on how to appropriately add more than one group of data.
- See the example data for templates
The evaluate_project.R reads YAML DTS project files, as well as visualizes and statistically evaluates the data. The output of the file is reported in HTML.
- In RStudio, run the evaluate_project.R file by clicking the "Source" button. A user input will ask the user to select the project YAML file. While the code is running, the progress and an estimated completion time will be shown in the plots window. HTML evaluation sheets will be created in the saem folder as the xml data files.
| Error | Suggested solution |
|---|---|
| Error: You have selected files with non-equal metadata. Please check the file(s) above for consistency!" | The evaluate_project.R checks for matching metadata between the data files. In case of mismatching metadata an error message will display which ones are differing. |
| "Error: XML-content does not seem to be XML" | Make sure all xml files exist in the data folder, check for potential spelling errors in the filename and that the .xml file extension has been added to all files |
| No group comparison HTML outputs | Check that the data heading in single/two/three.groups is set to 1. |
| "Error: In file(filename, "r", encoding = encoding) : cannot open file 'readXMLdatafile.R': No such file or directory" | Make sure the right working directory is selected |
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