Categorical scatterplots with R for biologists: a step-by-step guide

Benjamin Petre1, Aurore Coince2, Sophien Kamoun1

1 The Sainsbury Laboratory, Norwich, UK; 2 Earlham Institute, Norwich, UK

Weissgerber and colleagues (2015) recently stated that ‘as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies’. They called for more scatterplot and boxplot representations in scientific papers, which ‘allow readers to critically evaluate continuous data’ (Weissgerber et al., 2015). In the Kamoun Lab at The Sainsbury Laboratory, we recently implemented a protocol to generate categorical scatterplots (Petre et al., 2016; Dagdas et al., 2016). Here we describe the three steps of this protocol: 1) formatting of the data set in a .csv file, 2) execution of the R script to generate the graph, and 3) export of the graph as a .pdf file.

Protocol

• Step 1: format the data set as a .csv file. Store the data in a three-column excel file as shown in Powerpoint slide. The first column ‘Replicate’ indicates the biological replicates. In the example, the month and year during which the replicate was performed is indicated. The second column ‘Condition’ indicates the conditions of the experiment (in the example, a wild type and two mutants called A and B). The third column ‘Value’ contains continuous values. Save the Excel file as a .csv file (File -> Save as -> in ‘File Format’, select .csv). This .csv file is the input file to import in R.

• Step 2: execute the R script (see Notes 1 and 2). Copy the script shown in Powerpoint slide and paste it in the R console. Execute the script. In the dialog box, select the input .csv file from step 1. The categorical scatterplot will appear in a separate window. Dots represent the values for each sample; colors indicate replicates. Boxplots are superimposed; black dots indicate outliers.

• Step 3: save the graph as a .pdf file. Shape the window at your convenience and save the graph as a .pdf file (File -> Save as). See Powerpoint slide for an example.

Notes

• Note 1: install the ggplot2 package. The R script requires the package ‘ggplot2’ to be installed. To install it, Packages & Data -> Package Installer -> enter ‘ggplot2’ in the Package Search space and click on ‘Get List’. Select ‘ggplot2’ in the Package column and click on ‘Install Selected’. Install all dependencies as well.

• Note 2: use a log scale for the y-axis. To use a log scale for the y-axis of the graph, use the command line below in place of command line #7 in the script.

7 Display the graph in a separate window. Dot colors indicate

replicates

graph + geom_boxplot(outlier.colour='black', colour='black') + geom_jitter(aes(col=Replicate)) + scale_y_log10() + theme_bw()

References

Dagdas YF, Belhaj K, Maqbool A, Chaparro-Garcia A, Pandey P, Petre B, et al. (2016) An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor. eLife 5:e10856.

Petre B, Saunders DGO, Sklenar J, Lorrain C, Krasileva KV, Win J, et al. (2016) Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies. PLoS ONE 11(2):e0149035

Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015) Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLoS Biol 13(4):e1002128

https://cran.r-project.org/

http://ggplot2.org/

This paper introduces the sparse functional boxplot and the intensity sparse functional boxplot as practical exploratory tools. Besides being available for complete functional data, they can be used in sparse univariate and multivariate functional data. The sparse functional boxplot, based on the functional boxplot, displays sparseness proportions within the 50% central region. The intensity sparse functional boxplot indicates the relative intensity of fitted sparse point patterns in the central region. The two-stage functional boxplot, which derives from the functional boxplot to detect outliers, is furthermore extended to its sparse form. We also contribute to sparse data fitting improvement and sparse multivariate functional data depth. In a simulation study, we evaluate the goodness of data fitting, several depth proposals for sparse multivariate functional data, and compare the results of outlier detection between the sparse functional boxplot and its two-stage version. The practical applications of the sparse functional boxplot and intensity sparse functional boxplot are illustrated with two public health datasets. Supplementary materials and codes are available for readers to apply our visualization tools and replicate the analysis.

The Florida Flood Hub for Applied Research and Innovation and the U.S. Geological Survey have developed projected future change factors for precipitation depth-duration-frequency (DDF) curves at 242 National Oceanic and Atmospheric Administration (NOAA) Atlas 14 stations in Florida. The change factors were computed as the ratio of projected future to historical extreme-precipitation depths fitted to extreme-precipitation data from downscaled climate datasets using a constrained maximum likelihood (CML) approach as described in https://doi.org/10.3133/sir20225093. The change factors correspond to the periods 2020-59 (centered in the year 2040) and 2050-89 (centered in the year 2070) as compared to the 1966-2005 historical period. An R script (basin_boxplot.R) is provided as an example on how to create a wrapper function that will automate the generation of boxplots of change factors for all Florida HUC-8 basins. The wrapper script sources the file create_boxplot.R and calls the function create_boxplot() one Florida basin at a time to create a figure with boxplots of change factors for all durations (1, 3, and 7 days) and return periods (5, 10, 25, 50, 100, 200, and 500 years) evaluated as part of this project. An example is also provided in the code that shows how to generate a figure showing boxplots of change factors for a single duration and return period. A Microsoft Word file documenting code usage is also provided within this data release (Documentation_R_script_create_boxplot.docx). As described in the documentation, the R script relies on some of the Microsoft Excel spreadsheets published as part of this data release. The script uses HUC-8 basins defined in the "Florida Hydrologic Unit Code (HUC) Basins (areas)" from the Florida Department of Environmental Protection (FDEP; https://geodata.dep.state.fl.us/datasets/FDEP::florida-hydrologic-unit-code-huc-basins-areas/explore) and their names are listed in the file basins_list.txt provided with the script. County names are listed in the file counties_list.txt provided with the script. NOAA Atlas 14 stations located in each Florida basin or county are defined in the Microsoft Excel spreadsheet Datasets_station_information.xlsx which is part of this data release. Instructions are provided in code documentation (see highlighted text on page 7 of Documentation_R_script_create_boxplot.docx) so that users can modify the script to generate boxplots for basins different from the FDEP "Florida Hydrologic Unit Code (HUC) Basins (areas)."

The South Florida Water Management District (SFWMD) and the U.S. Geological Survey have developed projected future change factors for precipitation depth-duration-frequency (DDF) curves at 174 National Oceanic and Atmospheric Administration (NOAA) Atlas 14 stations in central and south Florida. The change factors were computed as the ratio of projected future to historical extreme precipitation depths fitted to extreme precipitation data from various downscaled climate datasets using a constrained maximum likelihood (CML) approach. The change factors correspond to the period 2050-2089 (centered in the year 2070) as compared to the 1966-2005 historical period. An R script (create_boxplot.R) is provided which generates boxplots of change factors by NOAA Atlas 14 station, or for all NOAA Atlas 14 stations in an ArcHydro Enhanced Database (AHED) basin or county. In addition, the R script basin_boxplot.R is provided as an example on how to create a wrapper function that will automate the generation of boxplots of change factors for all AHED basins. This Microsoft Word file (Documentation_R_script_create_boxplot.docx) serves as documentation on the code usage and available options for running the scripts. As described in the documentation, the R scripts rely on some of the Microsoft Excel spreadsheets published as part of this data release.

This dataset contains the prioritization provided by a panel of 15 experts to a set of 28 barriers categories for 8 different roles of the future energy system. A Delphi method was followed and the scores provided in the three rounds carried out are included. The dataset also contains the scripts used to assess the results and the output of this assessment. A list of the information contained in this file is: data folder: this folders includes the scores given by the 15 experts in the 3 rounds. Every round is in an individual folder. There is a file per expert that has the scores between -5 (not relevant at all) to 5 (completely relevant) per barrier (rows) and actor (columns). There is also a file with the description of the experts in terms of their position in the company, the type of company and the country. fig folder: this folder includes the figures created to assess the information provided by the experts. For each round, the following figures are created (in each respective folder): Boxplot with the distribution of scores per barriers and roles. Heatmap with the mean scores per barriers and roles. Boxplots with the comparison of the different distributions provided by the experts of each group (depending on the keywords) per barrier and role. Heatmap with the mean score per barrier and use case and with the prioritization per barrier and use case. Finally, bar plots with the mean scores differences between rounds and boxplot with comparisons of the scores distributions are also provided. stat folder: this folder includes the files with the results of the different statistical assessment carried out. For each round, the following figures are created (in each respective folder): The statistics used to assess the scores (Intraclass correlation coefficient, Inter-rater agreement, Inter-rater agreement p-value, Homogeneity of Variances, Average interquartile range, Standard Deviation of interquartile ranges, Friedman test p-value Average power post hoc) per barrier and per role. The results of the post hoc of the Friedman Test per berries and per roles. The average score per barrier and per role. The mean value of the scores provided by the experts grouped by the keywords per barrier and role. P-value of the comparison of these two values. The end prioritization of the barrier for the use case (averaging the scores or merging the critical sets) Finally, the differences between the mean and standard deviations of the scores between two consecutive rounds are provided.

Sheet 1 (Raw-Data): The raw data of the study is provided, presenting the tagging results for the used measures described in the paper. For each subject, it includes multiple columns: A. a sequential student ID B an ID that defines a random group label and the notation C. the used notation: user Story or use Cases D. the case they were assigned to: IFA, Sim, or Hos E. the subject's exam grade (total points out of 100). Empty cells mean that the subject did not take the first exam F. a categorical representation of the grade L/M/H, where H is greater or equal to 80, M is between 65 included and 80 excluded, L otherwise G. the total number of classes in the student's conceptual model H. the total number of relationships in the student's conceptual model I. the total number of classes in the expert's conceptual model J. the total number of relationships in the expert's conceptual model K-O. the total number of encountered situations of alignment, wrong representation, system-oriented, omitted, missing (see tagging scheme below) P. the researchers' judgement on how well the derivation process explanation was explained by the student: well explained (a systematic mapping that can be easily reproduced), partially explained (vague indication of the mapping ), or not present.

Tagging scheme:
Aligned (AL) - A concept is represented as a class in both models, either

with the same name or using synonyms or clearly linkable names; Wrongly represented (WR) - A class in the domain expert model is incorrectly represented in the student model, either (i) via an attribute, method, or relationship rather than class, or (ii) using a generic term (e.g., user'' instead ofurban planner''); System-oriented (SO) - A class in CM-Stud that denotes a technical implementation aspect, e.g., access control. Classes that represent legacy system or the system under design (portal, simulator) are legitimate; Omitted (OM) - A class in CM-Expert that does not appear in any way in CM-Stud; Missing (MI) - A class in CM-Stud that does not appear in any way in CM-Expert.

All the calculations and information provided in the following sheets

originate from that raw data.

Sheet 2 (Descriptive-Stats): Shows a summary of statistics from the data collection,

including the number of subjects per case, per notation, per process derivation rigor category, and per exam grade category.

Sheet 3 (Size-Ratio):

The number of classes within the student model divided by the number of classes within the expert model is calculated (describing the size ratio). We provide box plots to allow a visual comparison of the shape of the distribution, its central value, and its variability for each group (by case, notation, process, and exam grade) . The primary focus in this study is on the number of classes. However, we also provided the size ratio for the number of relationships between student and expert model.

Sheet 4 (Overall):

Provides an overview of all subjects regarding the encountered situations, completeness, and correctness, respectively. Correctness is defined as the ratio of classes in a student model that is fully aligned with the classes in the corresponding expert model. It is calculated by dividing the number of aligned concepts (AL) by the sum of the number of aligned concepts (AL), omitted concepts (OM), system-oriented concepts (SO), and wrong representations (WR). Completeness on the other hand, is defined as the ratio of classes in a student model that are correctly or incorrectly represented over the number of classes in the expert model. Completeness is calculated by dividing the sum of aligned concepts (AL) and wrong representations (WR) by the sum of the number of aligned concepts (AL), wrong representations (WR) and omitted concepts (OM). The overview is complemented with general diverging stacked bar charts that illustrate correctness and completeness.

For sheet 4 as well as for the following four sheets, diverging stacked bar

charts are provided to visualize the effect of each of the independent and mediated variables. The charts are based on the relative numbers of encountered situations for each student. In addition, a "Buffer" is calculated witch solely serves the purpose of constructing the diverging stacked bar charts in Excel. Finally, at the bottom of each sheet, the significance (T-test) and effect size (Hedges' g) for both completeness and correctness are provided. Hedges' g was calculated with an online tool: https://www.psychometrica.de/effect_size.html. The independent and moderating variables can be found as follows:

Sheet 5 (By-Notation):

Model correctness and model completeness is compared by notation - UC, US.

Sheet 6 (By-Case):

Model correctness and model completeness is compared by case - SIM, HOS, IFA.

Sheet 7 (By-Process):

Model correctness and model completeness is compared by how well the derivation process is explained - well explained, partially explained, not present.

Sheet 8 (By-Grade):

Model correctness and model completeness is compared by the exam grades, converted to categorical values High, Low , and Medium.

Effective communication of radiation exposure data is essential for improving safety management practices for radiological workers. However, traditional tabular formats used in reporting radiation exposure data often fail to convey critical patterns and trends, making it difficult for non-experts to interpret and act on the information. This study evaluates the application of data visualization techniques, including radar charts, box plots, sparklines, and Chernoff faces, to enhance the accessibility and comprehension of radiation exposure data. Using datasets from the “2022 Annual Report on Individual Exposure Doses of Radiological Workers” published by the KDCA, this study demonstrates how visualization can effectively highlight disparities across professions, demographic groups, and geographic regions. The findings underscore the significant potential of visualization methods in simplifying complex datasets, enabling stakeholders to make more informed decisions. Nonetheless, the study has limitations, including its reliance on pre-existing public datasets and a lack of real-time or granular data. Future research should focus on collecting primary data to explore causal relationships in radiation exposure trends and on applying advanced statistical and machine learning techniques to uncover deeper insights. By integrating robust visualization methods, this study aims to bridge the gap between raw data and actionable knowledge, ultimately contributing to safer occupational environments for radiological workers.