shrink_df: Shrink data.frame by row groups
In jmw86069/jamses: Jam SummarizedExperiment Stats

shrink_df

R Documentation

Shrink data.frame by row groups

Description

Shrink data.frame by row groups

Usage

shrink_df(
  x,
  by,
  string_func = function(x) jamba::cPasteSU(x, na.rm = TRUE),
  num_func = function(x) mean(x, na.rm = TRUE),
  add_string_cols = NULL,
  num_to_string_func = as.character,
  keep_na_groups = TRUE,
  include_num_reps = FALSE,
  extra_funcs = NULL,
  do_test = FALSE,
  use_new_method = FALSE,
  verbose = FALSE,
  ...
)

Arguments

`by`	`character` vector of one or more `colnames(df)`, used to define the row grouping.
`string_func`	`function` used for `character` and other non-numeric column types. For efficiency, `string_func` by default is applied to the entire column, with `list` input, expecting `vector` output. It is not applied using `data.table`.
`num_func`	`function` used for `numeric` column types. This function is applied using `data.table` and should expect a `vector` input, and provide a single atomic value output.
`extra_funcs`	`list`, default `NULL`, containing `function` objects. The list names should match `colnames(x)`, in order to apply a function to a specific column in `x`. These functions will therefore override the default functions defined by `string_func` and `num_func`. Only one function is applied per column.
`do_test`	`logical`, default FALSE, indicating whether to perform an internal test with internally-generated argument values.
`use_new_method`	`logical` default FALSE, whether to call newer tidy/data.table methods (TRUE), or call `shrinkDataFrame()` (FALSE). Currently `shrinkDataFrame()` is remarkably faster. More research necessary.
`verbose`	`logical` indicating whether to print verbose output.
`...`	additional arguments are ignored.
`df`	`data.frame` or compatible input class.

Details

This function is currently a wrapper for shrinkDataFrame(), it was formerly a simplified version of shrinkDataFrame() which is intended to use more modern methods from the R package data.table.

The general idea is to collapse numeric columns using num_func, and collapse character and all other columns using string_func.

Any exceptions, where a different function should be applied, are passed via argument extra_funcs which is a list of functions named by values in colnames(df).

Other jamses utilities: choose_annotation_colnames(), contrast2comp_dev(), fold_to_log2fold(), intercalate(), list2im_opt(), log2fold_to_fold(), make_block_arrow_polygon(), mark_stat_hits(), matrix_normalize(), point_handedness(), point_slope_intercept(), shortest_unique_abbreviation(), shrinkDataFrame(), shrink_matrix(), sort_samples(), strsplitOrdered(), sub_split_vector(), update_function_params(), update_list_elements()