Figures in scientific publications are critically important because they often show the data supporting key findings. Our systematic review of research articles published in top physiology journals (n = 703) suggests that, as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies. Papers rarely included scatterplots, box plots, and histograms that allow readers to critically evaluate continuous data. Most papers presented continuous data in bar and line graphs. This is problematic, as many different data distributions can lead to the same bar or line graph. The full data may suggest different conclusions from the summary statistics. We recommend training investigators in data presentation, encouraging a more complete presentation of data, and changing journal editorial policies. Investigators can quickly make univariate scatterplots for small sample size studies using our Excel templates.

Time-Series Matrix (TSMx): A visualization tool for plotting multiscale temporal trends TSMx is an R script that was developed to facilitate multi-temporal-scale visualizations of time-series data. The script requires only a two-column CSV of years and values to plot the slope of the linear regression line for all possible year combinations from the supplied temporal range. The outputs include a time-series matrix showing slope direction based on the linear regression, slope values plotted with colors indicating magnitude, and results of a Mann-Kendall test. The start year is indicated on the y-axis and the end year is indicated on the x-axis. In the example below, the cell in the top-right corner is the direction of the slope for the temporal range 2001–2019. The red line corresponds with the temporal range 2010–2019 and an arrow is drawn from the cell that represents that range. One cell is highlighted with a black border to demonstrate how to read the chart—that cell represents the slope for the temporal range 2004–2014. This publication entry also includes an excel template that produces the same visualizations without a need to interact with any code, though minor modifications will need to be made to accommodate year ranges other than what is provided. TSMx for R was developed by Georgios Boumis; TSMx was originally conceptualized and created by Brad G. Peter in Microsoft Excel. Please refer to the associated publication: Peter, B.G., Messina, J.P., Breeze, V., Fung, C.Y., Kapoor, A. and Fan, P., 2024. Perspectives on modifiable spatiotemporal unit problems in remote sensing of agriculture: evaluating rice production in Vietnam and tools for analysis. Frontiers in Remote Sensing, 5, p.1042624. https://www.frontiersin.org/journals/remote-sensing/articles/10.3389/frsen.2024.1042624 TSMx sample chart from the supplied Excel template. Data represent the productivity of rice agriculture in Vietnam as measured via EVI (enhanced vegetation index) from the NASA MODIS data product (MOD13Q1.V006). TSMx R script: # import packages library(dplyr) library(readr) library(ggplot2) library(tibble) library(tidyr) library(forcats) library(Kendall) options(warn = -1) # disable warnings # read data (.csv file with "Year" and "Value" columns) data <- read_csv("EVI.csv") # prepare row/column names for output matrices years <- data %>% pull("Year") r.names <- years[-length(years)] c.names <- years[-1] years <- years[-length(years)] # initialize output matrices sign.matrix <- matrix(data = NA, nrow = length(years), ncol = length(years)) pval.matrix <- matrix(data = NA, nrow = length(years), ncol = length(years)) slope.matrix <- matrix(data = NA, nrow = length(years), ncol = length(years)) # function to return remaining years given a start year getRemain <- function(start.year) { years <- data %>% pull("Year") start.ind <- which(data[["Year"]] == start.year) + 1 remain <- years[start.ind:length(years)] return (remain) } # function to subset data for a start/end year combination splitData <- function(end.year, start.year) { keep <- which(data[['Year']] >= start.year & data[['Year']] <= end.year) batch <- data[keep,] return(batch) } # function to fit linear regression and return slope direction fitReg <- function(batch) { trend <- lm(Value ~ Year, data = batch) slope <- coefficients(trend)[[2]] return(sign(slope)) } # function to fit linear regression and return slope magnitude fitRegv2 <- function(batch) { trend <- lm(Value ~ Year, data = batch) slope <- coefficients(trend)[[2]] return(slope) } # function to implement Mann-Kendall (MK) trend test and return significance # the test is implemented only for n>=8 getMann <- function(batch) { if (nrow(batch) >= 8) { mk <- MannKendall(batch[['Value']]) pval <- mk[['sl']] } else { pval <- NA } return(pval) } # function to return slope direction for all combinations given a start year getSign <- function(start.year) { remaining <- getRemain(start.year) combs <- lapply(remaining, splitData, start.year = start.year) signs <- lapply(combs, fitReg) return(signs) } # function to return MK significance for all combinations given a start year getPval <- function(start.year) { remaining <- getRemain(start.year) combs <- lapply(remaining, splitData, start.year = start.year) pvals <- lapply(combs, getMann) return(pvals) } # function to return slope magnitude for all combinations given a start year getMagn <- function(start.year) { remaining <- getRemain(start.year) combs <- lapply(remaining, splitData, start.year = start.year) magns <- lapply(combs, fitRegv2) return(magns) } # retrieve slope direction, MK significance, and slope magnitude signs <- lapply(years, getSign) pvals <- lapply(years, getPval) magns <- lapply(years, getMagn) # fill-in output matrices dimension <- nrow(sign.matrix) for (i in 1:dimension) { sign.matrix[i, i:dimension] <- unlist(signs[i]) pval.matrix[i, i:dimension] <- unlist(pvals[i]) slope.matrix[i, i:dimension] <- unlist(magns[i]) } sign.matrix <-...

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/

To create the dataset, the top 10 countries leading in the incidence of COVID-19 in the world were selected as of October 22, 2020 (on the eve of the second full of pandemics), which are presented in the Global 500 ranking for 2020: USA, India, Brazil, Russia, Spain, France and Mexico. For each of these countries, no more than 10 of the largest transnational corporations included in the Global 500 rating for 2020 and 2019 were selected separately. The arithmetic averages were calculated and the change (increase) in indicators such as profitability and profitability of enterprises, their ranking position (competitiveness), asset value and number of employees. The arithmetic mean values of these indicators for all countries of the sample were found, characterizing the situation in international entrepreneurship as a whole in the context of the COVID-19 crisis in 2020 on the eve of the second wave of the pandemic. The data is collected in a general Microsoft Excel table. Dataset is a unique database that combines COVID-19 statistics and entrepreneurship statistics. The dataset is flexible data that can be supplemented with data from other countries and newer statistics on the COVID-19 pandemic. Due to the fact that the data in the dataset are not ready-made numbers, but formulas, when adding and / or changing the values in the original table at the beginning of the dataset, most of the subsequent tables will be automatically recalculated and the graphs will be updated. This allows the dataset to be used not just as an array of data, but as an analytical tool for automating scientific research on the impact of the COVID-19 pandemic and crisis on international entrepreneurship. The dataset includes not only tabular data, but also charts that provide data visualization. The dataset contains not only actual, but also forecast data on morbidity and mortality from COVID-19 for the period of the second wave of the pandemic in 2020. The forecasts are presented in the form of a normal distribution of predicted values and the probability of their occurrence in practice. This allows for a broad scenario analysis of the impact of the COVID-19 pandemic and crisis on international entrepreneurship, substituting various predicted morbidity and mortality rates in risk assessment tables and obtaining automatically calculated consequences (changes) on the characteristics of international entrepreneurship. It is also possible to substitute the actual values identified in the process and following the results of the second wave of the pandemic to check the reliability of pre-made forecasts and conduct a plan-fact analysis. The dataset contains not only the numerical values of the initial and predicted values of the set of studied indicators, but also their qualitative interpretation, reflecting the presence and level of risks of a pandemic and COVID-19 crisis for international entrepreneurship.

This dataset contains all current and active business licenses issued by the Department of Business Affairs and Consumer Protection. This dataset contains a large number of records /rows of data and may not be viewed in full in Microsoft Excel. Therefore, when downloading the file, select CSV from the Export menu. Open the file in an ASCII text editor, such as Notepad or Wordpad, to view and search.

Data fields requiring description are detailed below.

APPLICATION TYPE: 'ISSUE' is the record associated with the initial license application. 'RENEW' is a subsequent renewal record. All renewal records are created with a term start date and term expiration date. 'C_LOC' is a change of location record. It means the business moved. 'C_CAPA' is a change of capacity record. Only a few license types my file this type of application. 'C_EXPA' only applies to businesses that have liquor licenses. It means the business location expanded.

LICENSE STATUS: 'AAI' means the license was issued.

Business license owners may be accessed at: http://data.cityofchicago.org/Community-Economic-Development/Business-Owners/ezma-pppn To identify the owner of a business, you will need the account number or legal name.

Data Owner: Business Affairs and Consumer Protection

Time Period: Current

Frequency: Data is updated daily

The Global Environment Outlook (GEO) Data Portal was initiated in October 2000 to provide a comprehensive, reliable, and timely supply of data sets used by the United Nations Environment Programme (UNEP) and its partners in the GEO reports and other integrated environment assessments. Since then, the GEO Data Portal has matured into a unique data and information application which responds to the needs of the global environmental community for easy access to systematic and well-documented data on the environment, including the state of natural resources, as well as the societal driving forces and root causes of environmental change and degradation.

The GEO Data Portal is managed by DEWA/GRID-Geneva which is part of UNEP's global network of environmental information centres, known as the Global Resource Information Database (GRID).

The GEO Data Portal's online database holds more than 700 data sets representing over 400 unique variables. Data are provided as national, subregional, regional and global statistics or as geospatial data sets (maps), covering themes like Freshwater, Population, Forests, Emissions, Climate, Disasters, Health, and Gross Domestic Product (GDP). The data cover the time period from 1972-2002 where available. The GEO Data Portal offers users the option to: (1) draw, view and explore maps, graphs and tables online; (2) view documentation and other metadata; and/or (3) download data sets as Excel, PDF, CSV, XML or ARCINFO Shape files as appropriate.

Data from the GEO Data Portal are extracted by UNEP/DEWA/GRID-Geneva to produce another product, called the GEO-3 Data Compendium. The Compendium provides the major statistical data sets underlying the integrated analyses in the GEO reports. It is available online at [http://geocompendium.grid.unep.ch/] as well as on CD-ROM and as a printed publication.

The latest GEO report is GEO-3. This third edition complements the detailed assessment of the state of the global environment set out in GEO-2000.

The data sets held in the GEO Data Portal are derived from many different organizations and databases. These sources are listed at [http://geodata.grid.unep.ch/datasource.php]. In addition to providing readily available data sets, several institutions also have assisted in data processing. The data sources and providers are listed in the metadata that accompany each data set.

Data for each graph (C, D, D’, E, F, F’, G, H, J, K) is given in a separate sheet containing raw data values of x and y axes, along with the corresponding cell and embryo identifier for each data point when appropriate (cell identifier and embryo name, respectively). Each sheet is labelled with the relevant figure panel number. (XLSB)

Data for graph (E) is given in a separate sheet containing raw data values of x and y axes, along with the corresponding cell and embryo identifier for each data point when appropriate (cell identifier and embryo name, respectively). The sheet is labelled with the relevant figure panel number. (XLSB)

The dataset includes a total of 2 independent data files, of which (1) text data is an Excel dataset, including 3 Excel files with a total of 486 pieces of data, containing 215 pieces of data on weekly shipment of fresh eggs by provinces (municipalities directly under the central government and autonomous regions) from 2018-2022, annual shipment and year-on-year rate of change of fresh eggs by the whole country and by provinces (municipalities directly under the central government and autonomous regions) from 2018-2022 10 data, and 261 data on weekly fresh egg shipments and year-on-year rate of change in the main marketing areas of fresh eggs nationwide, 2018-2022; (2) the image data is a picture dataset with a total of 109 pictures, including 75 line graphs of changes in weekly fresh egg shipments across the country and 15 provinces (municipalities directly under the central government and autonomous regions), 32 line graphs of yearly fresh egg shipments across the country and 15 provinces (municipalities directly under the central government and autonomous regions) and year-on-year rate of change in fresh egg shipments nationwide.32 line graphs, 2 line graphs of weekly fresh egg shipments and year-on-year change rate in the main marketing areas of the country.

This MS Excel data has been processed into line graphs to create time series line graphs and data tables which give insight into changing physiochemical water quality characteristics and influences. The study sets out to determine if climate change has had an influence on physiochemical water quality characteristics both within and between the Breede and Olifants estuaries over a nine year monitoring period. The data represents changes and comparisons between salinity, temperature and rainfall within and between the Olifants and Breede river estuaries in the Wester Cape Province of South Africa.

Brent fell to 69.48 USD/Bbl on August 1, 2025, down 3.10% from the previous day. Over the past month, Brent's price has risen 0.54%, but it is still 9.54% lower than a year ago, according to trading on a contract for difference (CFD) that tracks the benchmark market for this commodity. Brent crude oil - values, historical data, forecasts and news - updated on August of 2025.

Data for each graph (A, A’, C, D) is given in a separate sheet containing raw data values of x and y axes, along with the corresponding cell and embryo identifier for each data point when appropriate (cell identifier and embryo name, respectively). Each sheet is labelled with the relevant figure panel number. (XLSB)

Data for each graph (A, B, C, D, E, F) is given in a separate sheet containing raw data values of x and y axes, along with the corresponding cell and embryo identifier for each data point when appropriate (cell identifier and embryo name, respectively). Each sheet is labelled with the relevant figure panel number. (XLSB)

Graph and download economic data for NASDAQ 100 Index (NASDAQ100) from 1986-01-02 to 2025-08-01 about NASDAQ, stock market, indexes, and USA.