R/microRutils.R

In mwrowe/microRutils: Mike Rowe's Miscellaneous R Utility Functions

#' microRutils: Mike Rowe's Miscellaneous R Utility Functions
#' 
#' The microRutils package contains various functions for text manipulation,
#' plotting and general utility. These have been developed over the last decade
#' or so; they range from the picayune to the highly useful.
#'
#' @section General Utility:
#' \itemize{
#'    \item \code{\link{cbindSafe}(), \link{rbindSafe}()}:
#'        Column-/row-wise concatenation of objects with potentially
#'        different rows/columns.
#'    \item \code{\link{compressMatrix}()}:
#'        Resize a matrix by combining adjacent elements.
#'    \item \code{\link{express}()}:
#'        Programmatically generate expression objects.
#'    \item \code{\link{getLapplyIndex}()}:
#'        Access index of list element from within lapply().
#'    \item \code{\link{nameslike}()}:
#'        Find named elements, rows or columns using a regular expression.
#'    \item \code{\link{nonUniq}()}:
#'        Find replicated elements in a vector.
#'    \item \code{\link{numberReplicates}()}:
#'        Number recurring elements within a vector.
#'    \item \code{\link{Order}()}:
#'        Order items using columns of a data.frame as keys.
#'    \item \code{\link{prepDir}()}:
#'        Create a new directory.
#'    \item \code{\link{pvalOrder}()}:
#'        Order p-values by levels, then numeric value.
#'    \item \code{\link{rowMads}()}:
#'        Fast calculation of MADs by row.
#'    \item \code{\link{rowSds}()}:
#'        Fast calculation of standard deviations of rows.
#'    \item \code{\link{rowZs}()}:
#'        Fast calculation of Z-scores by row.
#'    \item \code{\link{samediff}()}:
#'        Find elements in common, and unique to, two vectors.
#'    \item \code{\link{selectRows}()}:
#'        Row selection of a data.frame.
#'    \item \code{\link{uniqRowFreqs}()}:
#'        Count occurrences of replicate rows in a data.frame.
#'    \item \code{\link{untab}()}:
#'        Convert a table object to an array.
#' }
#'
#' @section Text Manipulation:
#' \itemize{
#'    \item \code{\link{is.char}(), \link{as.char}()}:
#'        Alises for as.character() and is.character().
#'    \item \code{\link{asciiToChar}()}:
#'        Conversion between letters and ASCII codes.
#'    \item \code{\link{cString}()}:
#'        Create a c() expression from character vector.
#'    \item \code{\link{orString}()}:
#'        Generate an OR regular expression substring.
#'    \item \code{\link{p.print}()}:
#'        Formats p-values for readability.
#'    \item \code{\link{percent}()}:
#'        Format numeric values as (character) percentages.
#'    \item \code{\link{regextr}()}:
#'        Substring extraction by regular expression.
#'    \item \code{\link{rename}()}:
#'        Rename elements, rows or columns, etc. of an object.
#'    \item \code{\link{strrev}()}:
#'        Reverse character order within each element of a character vector.
#'    \item \code{\link{yyyymmdd}()}:
#'        Generate a formatted time stamp.
#' }
#'
#' @section Plotting Functions:
#' \itemize{
#'    \item \code{\link{circle}()}: Plot a circle or regular polygon.
#'    \item \link[microRutils:hot]{Custom colormaps for heat maps}:
#'       \code{aqua.brown(), grayscale, hot(), hot2(), jet(), orange.blue(),
#'       purple.green(), purple.orange(), red.green(), yellow.blue()}
#'    \item \code{\link{enclose.plot}()}:
#'        Draw edge around a plot.
#'    \item \code{\link{groupedTickLabels}()}:
#'        Label axes with hierarchically organized groups.
#'    \item \code{\link{Hist}()}:
#'        Modified version of the graphics::hist() histogram function.
#'    \item \code{\link{Image}()}:
#'        Modified version of the graphics::image() plotting function.
#'    \item \code{\link{logtix}()}:
#'        Add log-scaled tick marks to an axis.
#'    \item \code{\link{plot2Dhist}()}:
#'        Generate and plot a 2D-histogram as a heatmap.
#'    \item \code{\link{sym}()}:
#'        Get a numeric range that is symmetric around zero.
#'    \item \code{\link{T.width}()}:
#'        Determine width of caps on error bars as fraction of plot width.
#'    \item \code{\link{VennPlot}()}:
#'        Draw a Venn plot with proportional areas.
#'    \item \code{\link{x.pt}(), \link{y.pt}()}:
#'        Get the location value associated with a fraction of x- or y-axis.
#' }
#'
#' @docType package
#' @name microRutils
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