opm_files {opm}R Documentation

Files and colour sets used by the package

Description

Get list of files from the opm package of interest for the user or select from some predefined colour sets for plotting.

Usage

  opm_files(what = c("scripts", "testdata", "auxiliary", "demo", "doc", "css", "sql",
    "omnilog", "single", "multiple", "growth"))

  select_colors(set = c("w3c", "w3c.i", "w3c.r", "nora", "nora.i", "nora.r", "brewer",
    "brewer.i", "brewer.r", "roseo", "roseo.i", "roseo.r", "ssnot", "ssnot.i", "ssnot.r",
    "phrogz", "phrogz.i", "phrogz.r", "groups", "groups.i", "groups.r", "jp01", "jp01.i",
    "jp01.r", "jp02", "jp02.i", "jp02.r", "jp03", "jp03.i", "jp03.r", "jp04", "jp04.i",
    "jp04.r", "jp05", "jp05.i", "jp05.r", "jp06", "jp06.i", "jp06.r", "jp07", "jp07.i",
    "jp07.r", "jp08", "jp08.i", "jp08.r", "jp09", "jp09.i", "jp09.r", "jp10", "jp10.i",
    "jp10.r", "jp11", 
        "jp11.i", "jp11.r", "jp12", "jp12.i", "jp12.r", "jp13", "jp13.i", "jp13.r",
    "jp14", "jp14.i", "jp14.r", "jp15", "jp15.i", "jp15.r", "jp16", "jp16.i", "jp16.r",
    "jp17", "jp17.i", "jp17.r", "jp18", "jp18.i", "jp18.r", "jp19", "jp19.i", "jp19.r",
    "jp20", "jp20.i", "jp20.r", "jp21", "jp21.i", "jp21.r", "jp22", "jp22.i", "jp22.r",
    "jp23", "jp23.i", "jp23.r", "jp24", "jp24.i", "jp24.r", "jp25", "jp25.i", "jp25.r",
    "jp26", "jp26.i", "jp26.r", "jp27", "jp27.i", "jp27.r", "jp28", "jp28.i", "jp28.r",
    "jp29", 
        "jp29.i", "jp29.r", "jp30", "jp30.i", "jp30.r", "jp31", "jp31.i", "jp31.r",
    "jp32", "jp32.i", "jp32.r", "jp33", "jp33.i", "jp33.r", "jp34", "jp34.i", "jp34.r",
    "jp35", "jp35.i", "jp35.r", "jp36", "jp36.i", "jp36.r", "jp37", "jp37.i", "jp37.r",
    "jp38", "jp38.i", "jp38.r", "jp39", "jp39.i", "jp39.r", "jp40", "jp40.i", "jp40.r"))

Arguments

what

Character scalar indicating the subdirectory to search in or the kind of names to obtain. Currently the following subdirectories are included:

auxiliary

Miscellaneous files which are neither executable scripts nor test data.

css

Predefined CSS files for HTML files generated by, e.g., phylo_data.

doc

The vignette (documentation) in several formats, including the extracted R code.

demo

Example R code using the opm package that neither fitted into these help pages nor into the vignette. Can directly be loaded via demo; see demo(package = "opm").

growth

Growth-measurement example files.

multiple

Not directly readable (i.e., multiple-plate) test files.

omnilog

Directly readable (i.e., single-plate) test files from OmniLog(R) runs.

scripts

R script files for non-interactive uses of the opm package, particularly for the batch processing of many files. When called without input arguments or with the ‘-h’ switch, the scripts output usage information.

single

Directly readable (i.e., single-plate) test files.

sql

SQL files for working with relational databases.

testdata

Files as output by the devices such as the OmniLog(R) instrument. Included here as examples for data input (and metadata management).

set

Character scalar. Name of the colour vector to use. Colour vectors have been optimised for maximum contrast between adjacent colours, either manually or using max_rgb_contrast from the pkgutils package. Names ending in ‘.i’ indicate vectors in inverse order (compared to the vector with the same name except ‘.i’). Names ending in ‘.i’ indicate vectors in random order. For credits regarding the vectors see the code.

set can also be a numeric scalar, which is then used to select the set of colours thought to optimally yield contrasting colours for this number of items. Up to 40 items are supported.

Details

In addition to the results of ‘reserved.md.names’, it should be avoided to use metadata keys that start with a dot, as such keys might also be created intermediary by methods that have to compile metadata together with other information.

Note that pkg_files might fail with very unusual installations of the opm package.

See xy_plot for a usage example of select_colors. This function is not normally directly called by an opm user but could be used for testing before doing some serious plotting.

Value

Character vector of file names or reserved parameter names or names of colours.

References

http://www.colorbrewer.org

See Also

pkgutils::pkg_files utils::demo grDevices::colors grDevices::rainbow grDevices::grey

Other naming-functions: find_positions, find_substrate, gen_iii, listing, plate_type, register_plate, substrate_info, wells

Examples

## example input files
isRfile <- function(x) grepl("\\.R$", x, ignore.case = TRUE)
(x <- opm_files("auxiliary"))

## [1] "/usr/local/lib/R/library/opm/auxiliary/001_rdbms_drop.sql"  
## [2] "/usr/local/lib/R/library/opm/auxiliary/002_rdbms_create.sql"
## [3] "/usr/local/lib/R/library/opm/auxiliary/003_rdbms_delete.sql"
## [4] "/usr/local/lib/R/library/opm/auxiliary/styles_1.css"

stopifnot(!isRfile(x))
(x <- opm_files("demo"))

##  [1] "/usr/local/lib/R/library/opm/demo/MongoDB-IO.R"                  
##  [2] "/usr/local/lib/R/library/opm/demo/MySQL-IO.R"                    
##  [3] "/usr/local/lib/R/library/opm/demo/PostgreSQL-IO.R"               
##  [4] "/usr/local/lib/R/library/opm/demo/SQLite-IO.R"                   
##  [5] "/usr/local/lib/R/library/opm/demo/cluster-with-pvalues.R"        
##  [6] "/usr/local/lib/R/library/opm/demo/custom-PCA.R"                  
##  [7] "/usr/local/lib/R/library/opm/demo/distinguish-curve-topologies.R"
##  [8] "/usr/local/lib/R/library/opm/demo/identify-positive-reactions.R" 
##  [9] "/usr/local/lib/R/library/opm/demo/multiple-plate-types.R"        
## [10] "/usr/local/lib/R/library/opm/demo/phenotype-vs-genotype.R"       
## [11] "/usr/local/lib/R/library/opm/demo/workshop-part-1.R"             
## [12] "/usr/local/lib/R/library/opm/demo/workshop-part-2.R"             
## [13] "/usr/local/lib/R/library/opm/demo/workshop-part-3.R"             
## [14] "/usr/local/lib/R/library/opm/demo/workshop-part-4.R"             
## [15] "/usr/local/lib/R/library/opm/demo/workshop-part-5.R"

stopifnot(isRfile(x))
(x <- opm_files("scripts"))

## [1] "/usr/local/lib/R/library/opm/scripts/run_opm.R"

stopifnot(isRfile(x))
(x <- opm_files("testdata"))

##  [1] "/usr/local/lib/R/library/opm/testdata/Example_1.csv.xz"                 
##  [2] "/usr/local/lib/R/library/opm/testdata/Example_2.csv.xz"                 
##  [3] "/usr/local/lib/R/library/opm/testdata/Example_3.csv.xz"                 
##  [4] "/usr/local/lib/R/library/opm/testdata/Example_Ecoplate.csv.xz"          
##  [5] "/usr/local/lib/R/library/opm/testdata/Example_ID_run.csv.xz"            
##  [6] "/usr/local/lib/R/library/opm/testdata/Example_LIMS_Export.exl.xz"       
##  [7] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_1.csv.xz"       
##  [8] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_2.csv.xz"       
##  [9] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_3.csv.xz"       
## [10] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_Multiple.csv.xz"
## [11] "/usr/local/lib/R/library/opm/testdata/Example_Perkin_Elmer.txt.xz"      
## [12] "/usr/local/lib/R/library/opm/testdata/Example_TECAN.txt.xz"

stopifnot(!isRfile(x))
for (name in c("growth", "single", "multiple", "omnilog")) {
  print(y <- opm_files(name))
  stopifnot(y %in% x) # i.e., a subset of the set of all input example files
}

## [1] "/usr/local/lib/R/library/opm/testdata/Example_Perkin_Elmer.txt.xz"
## [2] "/usr/local/lib/R/library/opm/testdata/Example_TECAN.txt.xz"       
##  [1] "/usr/local/lib/R/library/opm/testdata/Example_1.csv.xz"           
##  [2] "/usr/local/lib/R/library/opm/testdata/Example_2.csv.xz"           
##  [3] "/usr/local/lib/R/library/opm/testdata/Example_3.csv.xz"           
##  [4] "/usr/local/lib/R/library/opm/testdata/Example_Ecoplate.csv.xz"    
##  [5] "/usr/local/lib/R/library/opm/testdata/Example_ID_run.csv.xz"      
##  [6] "/usr/local/lib/R/library/opm/testdata/Example_LIMS_Export.exl.xz" 
##  [7] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_1.csv.xz" 
##  [8] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_2.csv.xz" 
##  [9] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_3.csv.xz" 
## [10] "/usr/local/lib/R/library/opm/testdata/Example_Perkin_Elmer.txt.xz"
## [11] "/usr/local/lib/R/library/opm/testdata/Example_TECAN.txt.xz"       
## [1] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_Multiple.csv.xz"
## [1] "/usr/local/lib/R/library/opm/testdata/Example_1.csv.xz"          
## [2] "/usr/local/lib/R/library/opm/testdata/Example_2.csv.xz"          
## [3] "/usr/local/lib/R/library/opm/testdata/Example_3.csv.xz"          
## [4] "/usr/local/lib/R/library/opm/testdata/Example_LIMS_Export.exl.xz"
## [5] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_1.csv.xz"
## [6] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_2.csv.xz"
## [7] "/usr/local/lib/R/library/opm/testdata/Example_Old_Style_3.csv.xz"

# On UNIX systems you should be able to do this if Rscript and the optparse
# package are properly installed:
# invisible(sapply(paste("Rscript", opm_files()), system))
# ...and get the usage messages of all scripts.

# Check the names of the example files: they should be ok
(x <- pkgutils::clean_filenames(opm_files("testdata"), demo = TRUE))

## Attempted renamings:

## named character(0)

stopifnot(length(x) == 0)

## colours
(x <- select_colors("nora"))

##  [1] "midnightblue"   "darkred"        "darkgreen"      "orange"        
##  [5] "lightslateblue" "seashell4"      "saddlebrown"    "firebrick2"    
##  [9] "palevioletred3" "purple4"

(y <- select_colors("nora.i")) # same in reverse order

##  [1] "purple4"        "palevioletred3" "firebrick2"     "saddlebrown"   
##  [5] "seashell4"      "lightslateblue" "orange"         "darkgreen"     
##  [9] "darkred"        "midnightblue"

stopifnot(is.character(x), length(x) > 0L, identical(x, rev(y)))
[Package opm version 1.3.63 Index]