Package 'foodwebWrapper'

Title: Enhanced Wrapper to Show Which Functions Call What
Description: Enhances the functionality of the mvbutils::foodweb() program. The matrix-format output of the original program contains identical row names and column names, each name representing a retrieved function. This format is enhanced by using the find_funs() program [see Sebastian (2017) <https://sebastiansauer.github.io/finds_funs/>] to concatenate the package name to the function name. Each package is assigned a unique color, that is used to color code the text naming the packages and the functions. This color coding is extended to the entries of value "1" within the matrix, indicating the pattern of ancestor and descendent functions.
Authors: Barry Zeeberg [aut, cre]
Maintainer: Barry Zeeberg <[email protected]>
License: GPL (>= 2)
Version: 1.1.0
Built: 2025-02-13 03:58:21 UTC
Source: https://github.com/cran/foodwebWrapper

Help Index

addStyle

Description

insert tags into HTML code to implement rotating table text

Usage

addStyle(x, m, colorMap, pawn)

Arguments

x

character vector containing HTML code
m

character matrix containing table that is represented in x
colorMap

character array of colors
pawn

Boolean if TRUE use chess symbols rather than rectangles in html table

Value

returns modified HTML code

Examples

if(interactive()){
load("data/x_x2.RData")
load("data/x_m5.RData")
load("data/x_colorMap.RData")
y<-addStyle(x_x2,x_m5,x_colorMap,pawn=TRUE)
}

attachedFunctions

Description

print a list of attached packages and their functions for the user to select from

Usage

attachedFunctions(verbose)

Arguments

verbose

Boolean if TRUE output several user messages

Value

returns a list whose components are

  • l list of user-selected packages and corresponding functions

  • where character vector of selected packages

Examples

if(interactive()){
attachedFunctions(verbose=TRUE)
}

attachedFunctionsBatch

Description

same as attachedFunctions() but no user interaction needed

Usage

attachedFunctionsBatch(packs)

Arguments

packs

list of character strings containing the names of packages package name is like "pack", not like "package:pack"

Value

returns a list whose components are

  • l list of user-selected packages and corresponding functions

  • where character vector of selected packages

Examples

if(interactive()){
attachedFunctionsBatch(c("SherlockHolmes","textBoxPlacement"))
}

attachedPackages

Description

print a list of attached packages for the user to select from

Usage

attachedPackages()

Value

returns a character vector of selected packages

Examples

if(interactive()){
attachedPackages()
}

colorTag

Description

add tag to color function name in column 2, based on package in column 1

Usage

colorTag(v1, v2, nc, x, colorMap, pawn)

Arguments

v1

character vector first column of m (excluding first 2 entries of m)
v2

character vector second column of m (excluding first 2 entries of m)
nc

integer number of columns of m
x

return value of replaceRotTag()
colorMap

character array of colors
pawn

Boolean if TRUE use chess symbols rather than rectangles in html table

Details

v1 is first column of m (excluding first 2 entries of m) v2 is second column of m (excluding first 2 entries of m)

Value

returns

concatPackFunc2

Description

match the package names with the function names

Usage

concatPackFunc2(m, v)

Arguments

m

character matrix return value component $funmat of foodweb()
v

character vector of package names returned by find_funz()

Value

returns augmented character matrix m

Examples

if(interactive()){
load("data/x_x.RData")
load("data/x_v.RData")
m<-concatPackFunc2(x_x$funmat,x_v)
}

consolidate

Description

create a permutation list of package names for re-ordering rows and columns of matrix m, in decreasing order of function counts per package

Usage

consolidate(v)

Arguments

v

character vector of package names component of return value of find_funz()

Value

returns a list whose components are character vector for permuting order of m

Examples

if(interactive()){
load("data/x_v.RData")
l<-consolidate(x_v)
}

find_funz

Description

determine in which R package a function ‘resides’

Usage

find_funz(packs, rfuns)

Arguments

packs

list of character strings containing the names of the packages
rfuns

list of character strings containing the names of functions in packs to which the result is to be restricted

Value

returns vector of character strings, names are functions and values are packages

Examples

if(interactive()){
load("data/x_packages.RData")
load("data/x_funs.RData")
find_funz(packs=x_packages,rfuns=x_funs)
}

foodwebWrapper

Description

wrapper for the function foodweb() concatenate the R package name for each retrieved R function

Usage

foodwebWrapper(
  where = character(0),
  ofile = "~/foodwebWrapper.html",
  zeros = TRUE,
  pawn = FALSE,
  verbose = TRUE
)

Arguments

where

position(s) on search path, or an environment, or a list of environments
ofile

character string containing path name for output file
zeros

Boolean if TRUE delete rows and cols that contain all 0's
pawn

Boolean if TRUE use chess symbols rather than rectangles in html table
verbose

Boolean if TRUE output several user messages

Details

if where is missing, then the user is presented with the option of choosing from a list of attached packages

Value

foodweb returns an object of (S3) class foodweb. This has three components:

  • funmat a matrix of 0s and 1s showing what (row) calls what (column). The dimnames are the function names.

  • x shows the x-axis location of the centre of each function's name in the display, in par("usr") units

  • level shows the y-axis location of the centre of each function's name in the display, in par("usr") units. For small numbers of functions, this will be an integer; for larger numbers, there will some adjustment around the nearest integer

Examples

if(interactive()){
load("data/x_packages.RData")
ofile<-sprintf("%s/foodwebWrapper.html",tempdir())
foodwebWrapper(ofile=ofile)
foodwebWrapper(where=x_packages,ofile=ofile)
}

foodwebWrapper data sets

Description

foodwebWrapper data sets

Usage

data(funs_examples)

mapFunctionsColors

Description

map functions to color coding

Usage

mapFunctionsColors(row1, col1, colors)

Arguments

row1

character vector containing names of packages
col1

character vector containing names of packages
colors

character vector containing names of colors

Value

returns a character vector mapping colors to package names

Examples

if(interactive()){
colors<-c("darkmagenta","darkolivegreen","darkorange3","brown4","red","blue")
load("data/x_m3.RData")
colorMap<-mapFunctionsColors(x_m3[1,c(-1,-2)],x_m3[c(-1,-2),1],colors)
}

rearrangeM

Description

rearrange the order of rows or columns of matrix based on entries in a vector

Usage

rearrangeM(m, v2)

Arguments

m

character matrix return value of concatPackFunc2()
v2

list whose components are package names for permuting order of m, return value of consolidate()

Value

returns rearranged version of m

Examples

if(interactive()){
load("data/x_m.RData")
load("data/x_v2.RData")
m2<-rearrangeM(x_m,x_v2)
}

removeZeroRowsCols

Description

delete rows and cols of matrix m that contain all "0"s

Usage

removeZeroRowsCols(m)

Arguments

m

character matrix whose entries are either "0" or "1"

Value

returns an altered version of character matrix m with removed rows and columns

Examples

if(interactive()){
load("data/x_m2.RData")
m3<-removeZeroRowsCols(x_m2)
}

replaceRotTag

Description

insert html tags for rotating text

Usage

replaceRotTag(x, l, dims)

Arguments

x

return value of readLines(), HTML code containing data table
l

return values of spanTag()
dims

return value of dim()

Value

returns modified version of HTML code containing data table

Examples

if(interactive()){
load("data/x_x.RData")
load("data/x_l.RData")
load("data/x_m3.RData")
x<-replaceRotTag(x_x,x_l,dim(x_m3))
}

rotStyle

Description

add html style definition for rotation

Usage

rotStyle()

Value

returns character string containing html style definition for rotation

Examples

r<-rotStyle()

rotTag

Description

add html tag to rotate function name

Usage

rotTag(v1, v2, colorMap)

Arguments

v1

character vector containing first row of matrix m (excluding first 2 entries of m)
v2

character vector containing second row of matrix m (excluding first 2 entries of m)
colorMap

character array of colors

Details

see https://stackoverflow.com/questions/47261100/how-to-rotate-text-90-degrees-inline also need to increase height of row to accommodate rotated text see https://resultuniversity.com/html/html-table-width-height#:~:text=To%20set%20the%20height%20of%20a%20specific%20row%20in%20an,property%20in%20pixels%20or%20percentages.

Value

returns character vector containing inserted html tags

Examples

if(interactive()){
load("data/x_m5.RData")
load("data/x_colorMap.RData")
rt<-rotTag(x_m5[1,c(-1,-2)],x_m5[2,c(-1,-2)],x_colorMap)
}

spanTag

Description

Add html tag for package name to span multiple columns. Also insert hyperlink to CRAN package and function documentation.

Usage

spanTag(v, direction = "COLSPAN", colorMap)

Arguments

v

character vector representing first row of m (excluding first 2 entries of m)
direction

character string COLSPAN or ROWSPAN
colorMap

character array of colors

Details

see https://www.pierobon.org/html/span.htm#:~:text=Cells%20within%20HTML%20tables%20can,span%20more%20than%20one%20column.

Value

returns a list whose components are

  • u return value of unique(v)

  • tab return value of table(v)

  • v2 character vector modified version of v containing html span tags

Examples

if(interactive()){
load("data/x_m5.RData")
load("data/x_colorMap.RData")
l<-spanTag(x_m5[1,c(-1,-2)],"COLSPAN",x_colorMap)
}

foodwebWrapper data sets

Description

foodwebWrapper data sets

Usage

data(x_colorMap)

foodwebWrapper data sets

Description

foodwebWrapper data sets

Usage

data(x_examples)

foodwebWrapper data sets

Description

foodwebWrapper data sets

Usage

data(x_f)

foodwebWrapper data sets

Description

foodwebWrapper data sets

Usage

data(x_funs)

foodwebWrapper data sets

Description

foodwebWrapper data sets

Usage

data(x_m)

foodwebWrapper data sets

Description

foodwebWrapper data sets

Usage

data(x_m2)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_m3)

foodwebWrapper data sets

Description

foodwebWrapper data sets

Usage

data(x_m4)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_m5)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_packages)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_v)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_v2)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_where)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_x)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_x2)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_x3)

foodwebWrapper data sets

Description

foodwebWrapper data sets

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data(x_y)