Rocinante

A collection of custom R functions. Helper functions complementing the new CodeAndRoll2. Many functionalities were part of the formerly used CodeAndRoll (v1).

Installation

1.) Download Rocinante.R, save as local .R file, and source(~/path/to/Rocinante.R):

2.) Directly source from the web:

source("https://raw.githubusercontent.com/vertesy/Rocinante/main/R/Rocinante.R")

List of functions

• stry

  Silent try

• sourcePartial

  Source parts of another script. Source: https://stackoverflow.com/questions/26245554/execute-a-set-of-lines-from-another-r-file

• eucl.dist.pairwise

  Calculate pairwise euclidean distance

• sign.dist.pairwise

  Calculate absolute value of the pairwise euclidean distance

• rowACF

  RETURNS A LIST. Calculates the autocorrelation of each row of a numeric matrix / data frame.

• colACF

  RETURNS A LIST. Calculates the autocorrelation of each row of a numeric matrix / data frame.

• acf.exactLag

  Autocorrelation with exact lag

• rowACF.exactLag

  RETURNS A Vector for the “lag” based autocorrelation. Calculates the autocorrelation of each row of a numeric matrix / data frame.

• colACF.exactLag

  RETURNS A Vector for the “lag” based autocorrelation. Calculates the autocorrelation of each row of a numeric matrix / data frame.

• clip2clip.vector

  Copy from clipboard (e.g. excel) to a R-formatted vector to the clipboard

• clip2clip.commaSepString

  Read a comma separated string (e.g. list of gene names) and properly format it for R.

• write_clip.replace.dot

  Clipboard export for da wonderful countries with where “,” is the decimal

• view.head

  view the head of an object by console.

• view.head2

  view the head of an object by View().

• iidentical.names

  Test if names of two objects for being exactly equal

• iidentical

  Test if two objects for being exactly equal

• iidentical.all

  Test if two objects for being exactly equal.

• IfExistsAndTrue

  Internal function. Checks if a variable is defined, and its value is TRUE.

• memory.biggest.objects

  https://stackoverflow.com/questions/17218404/should-i-get-a-habit-of-removing-unused-variables-in-r

• link_google

  Parse google search query links to your list of gene symbols. Strings “prefix” and ““suffix” will be searched for together with each gene (“Human ID4 neurons”). See many additional services in DatabaseLinke.R.

• link_bing

  Parse bing search query links to your list of gene symbols. Strings “prefix” and ““suffix” will be searched for together with each gene (“Human ID4 neurons”). See many additional services in DatabaseLinke.R.

• GC_content

  GC-content of a string (frequency of G and C letters among all letters).

• printEveryN

  Report at every e.g. 1000

• ’%!in%’

• stopif2

  Stop script if the condition is met. You can parse anything (e.g. variables) in the message

• say

  Use system voice to notify (after a long task is done)

• sayy

  Use system voice to notify (after a long task is done)

• oo

  Open current working directory.

• unload

  Unload a package. Source: https://stackoverflow.com/questions/6979917/how-to-unload-a-package-without-restarting-r

• irequire

  Load a package. If it does not exist, try to install it from CRAN.

• legend.col

  Source: https://aurelienmadouasse.wordpress.com/2012/01/13/legend-for-a-continuous-color-scale-in-r/

• val2col

  This function converts a vector of values(“yourdata”) to a vector of color levels. One must define the number of colors. The limits of the color scale(“zlim”) or the break points for the color changes(“breaks”) can also be defined. When breaks and zlim are defined, breaks overrides zlim.

• richColors

  Alias for rich.colors in gplots

• Color_Check

  Display the colors encoded by the numbers / color-ID-s you pass on to this function

• colSums.barplot

  Draw a barplot from ColSums of a matrix.

• lm_equation_formatter

  Renders the lm() function’s output into a human readable text. (e.g. for subtitles)

• lm_equation_formatter2

  Renders the lm() function’s output into a human readable text. (e.g. for subtitles)

• lm_equation_formatter3

  Renders the lm() function’s output into a human readable text. (e.g. for subtitles)

• hist.XbyY

  Split a one variable by another. Calculates equal bins in splitby, and returns a list of the corresponding values in toSplit.

• panel.cor.pearson

  A function to display correlation values for pairs() function. Default is pearson correlation, that can be set to “kendall” or “spearman”.

• panel.cor.spearman

  A function to display correlation values for pairs() function. Default is pearson correlation, that can be set to “kendall” or “spearman”.

• quantile_breaks

  Quantile breakpoints in any data vector http://slowkow.com/notes/heatmap-tutorial/

• hclust.getOrder.row

  Extract ROW order from a pheatmap object.

• hclust.getOrder.col

  Extract COLUMN order from a pheatmap object.

• hclust.getClusterID.row

  Extract cluster ID’s for ROWS of a pheatmap object.

• hclust.getClusterID.col

  Extract cluster ID’s for COLUMNS of a pheatmap object.

• hclust.ClusterSeparatingLines.row

  Calculate the position of ROW separating lines between clusters in a pheatmap object.

• hclust.ClusterSeparatingLines.col

  Calculate the position of COLUMN separating lines between clusters in a pheatmap object.

• Gap.Postions.calc.pheatmap

  calculate gap positions for pheatmap, based a sorted annotation vector of categories

• matlabColors.pheatmap

  Create a Matlab-like color gradient using “colorRamps”.

• annot_col.create.pheatmap.vec

  For VECTORS. Auxiliary function for pheatmap. Prepares the 2 variables needed for “annotation_col” and “annotation_colors” in pheatmap

• annot_col.create.pheatmap.df

  For data frames. Auxiliary function for pheatmap. Prepares the 2 variables needed for “annotation_col” and “annotation_colors” in pheatmap

• annot_col.fix.numeric

  fix class and color annotation in pheatmap annotation data frame’s and lists.

• annot_row.create.pheatmap.df

  For data frames. Auxiliary function for pheatmap. Prepares the 2 variables needed for “annotation_col” and “annotation_colors” in pheatmap

• sourceGitHub

• # RemoveFinalSlash

• ww.set.OutDir

• backup

  make a backup of an object into global env. Scheme: obj > obj.bac

• list.dirs.depth.n

  list dirs recursive up to a certain level in R https://stackoverflow.com/questions/48297440/list-files-recursive-up-to-a-certain-level-in-r

• qHGNC

  Parse HGNC links to your list of gene symbols.

• NrAndPc

  Summary stat. text formatting for logical vectors (%, length)

• jjpegA4

  Setup an A4 size jpeg