| Version: | 1.1.0 |
| Date: | 2023-12-20 |
| Title: | Enhanced Wrapper to Show Which Functions Call What |
| Maintainer: | Barry Zeeberg <barryz2013@gmail.com> |
| Depends: | R (≥ 4.2.0) |
| LazyData: | true |
| Imports: | mvbutils, utils, tibble, dplyr, R2HTML, textshaping, magrittr, tidyverse, stringr |
| 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. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| VignetteBuilder: | knitr |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| RoxygenNote: | 7.2.3 |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2023-12-20 15:04:56 UTC; barryzeeberg |
| Author: | Barry Zeeberg [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2023-12-20 15:20:02 UTC |
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
Usage
data(x_m3)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_m4)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_m5)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_packages)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_v)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_v2)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_where)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_x)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_x2)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_x3)
foodwebWrapper data sets
Description
foodwebWrapper data sets
Usage
data(x_y)