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).