Most Giotto commands can accept several matrix classes (DelayedMatrix, SparseM, Matrix or base matrix). To facilitate this we provide flexible wrappers that dispatch to our preferred methods for these operations.
mean_flex(): analogous to mean().
rowSums_flex(): analogous to rowSums().
rowMeans_flex(): analogous to rowMeans().
colSums_flex(): analogous to colSums().
colMeans_flex(): analogous to colMeans().
cor_flex(): analogous to cor().
Giotto has a number of auxiliary or convenience functions that might help you to adapt your code or write new code for Giotto. We encourage you to use these small functions to maintain uniformity throughout the code.
lapply_flex(): analogous to lapply() and works for both windows and unix systems.
all_plots_save_function(): compatible with Giotto instructions and helps to automatically save generated plots.
plot_output_handler(): further wraps all_plots_save_function and includes handling for return_plot and show_plot and Giotto instructions checking.
determine_cores(): determine the number of cores to use if a user does not set this explicitly.
get_os(): identify the operating system.
update_giotto_params(): will catch and store the parameters for each used command on a giotto object.
wrap_txt(), wrap_msg(), etc: text and message formatting functions.
vmsg(): framework for Giotto’s verbosity-flagged messages.
package_check(): to check if a package exists, works for packages on CRAN, Bioconductor and Github.
Should be used within your contribution code if it requires the use of packages not in Giotto’s DESCRIPTION file’s depends imports section.
Has the additional benefit that it will suggest to the user how to download the package if it is not available. To keep the size of Giotto within limits we prefer not to add too many new hard dependencies (packages in Depends or Suggests).