‘cyt_splsda’: Fixed an error occurring when only one variable has VIP > 1 leading to not being able to conduct sPLS-DA analysis. Now, the function checks whether the number of VIP > 1 variables is below 2, if that is true the sPLS-DA model of VIP > 1 is skipped.
Fixed an issue with the ‘verbose’ argument of ‘cyt_splsda’ not working in overall analysis due to calling the wrong object.
‘cyt_errbp’ now uses ‘ggplot2’ with ‘facet_wrap’ to create multiple error-bar plots where the p-value and effect size labels are based on t-test comparisons between the groups.
‘cyt_errbp’, ‘cyt_bp’, ‘cyt_bp2’, and ‘cyt_skku’ received a minor theme update keeping the background white in scenarios where it may appear transparent due to using ‘theme_minimal()’.
Fixed some grammatical and spelling issues in the README file.
Vignette for the package now show plots generated that aren’t saved to PDF files. A temporary directory is not created anymore.
‘cyt_rf’, ‘cyt_splsda’, ‘cyt_ttest’, ‘cyt_dualflashplot’, and ‘cyt_volc’ now have a logical ‘verbose’ argument to print the output if user wants to. This is to ensure printed output in console can be easily suppressed.
‘cyt_xgb’ has a new logical argument called ‘print_results’ that works the same as the ‘verbose’ argument in other functions mentioned above.
Reverted the previous ‘verbose’ conditionals on plots from the functions mentioned above as they are essential to the output. For example, after creating a ggplot2 object of the plots, I have left ‘print(a)’ without a ‘verbose’ conditional statement.
Have removed the arguments for changing graphical parameters in ‘cyt_bp’, and ‘cyt_bp2’ so it no longer requires changes to the user’s graphical parameters.
Added a new ‘format_output’ argument to ‘cyt_anova’ and ‘cyt_ttest’ to format the output as a data frame which can be printed to show neat format, however still dependent on whether ‘verbose’ equals TRUE or FALSE.
‘cyt_rf’, ‘cyt_splsda’, and ‘cyt_xgb’ now has a ‘seed’ argument to set the seed for reproducibility.
Added references in description field of the DESCRIPTION file to the multivariate methods mentioned in the format ‘Authors (Year) <doi:…>’.
Updated examples from graphical parameters changing without resetting properly to now the graphical parameters reverting to original using ‘oldpar <- par(no.readonly = TRUE)’ in the beginning and par(oldpar) after execution of code.
Updated ‘getting_started.Rmd’ vignette where the files created and saved are now saved to a temporary directory using ‘tempdir()’ to avoid creating files in the user’s working directory. Additionally, the vignette now uses ‘oldpar <- par(no.readonly = TRUE)’ in the beginning and par(oldpar) after code execution to revert to original graphical parameters for the ‘cyt_errbp’ examples shown.
Fixed some general CRAN automated test issues.
Updated functions and examples to avoid generating PDF and PNG files during checks.
Functions now also generated plots within RStudio graphics device and provides the option to save the plots as PDF or PNG files depending on the function.
Since this is our initial submission, our NEWS.md contains a single entry indicating the initial release. We plan to provide more detailed change logs in subsequent versions.
This version is the development version of CytoProfile. We are preparing for the initial CRAN submission. Below are the features added in this version: