wells {opm}R Documentation

Listing of well names

Description

Get the names of the wells contained in an OPMX object. Optionally the full substrate names can be added in parentheses or brackets or used instead of the coordinate, and trimmed to a given length. The listing methods create a textual listing of the discretised values. (See do_disc for generating discretised data.) This is useful to describe OmniLog(R) phenotype microarray results in a scientific manuscript.

Usage

  ## S4 method for signature 'MOPMX'
listing(x, as.groups,
    cutoff = opm_opt("min.mode"), downcase = TRUE, full = TRUE,
    in.parens = FALSE, html = FALSE, sep = " ", ..., exact = TRUE,
    strict = TRUE) 
  ## S4 method for signature 'OPMD'
listing(x, as.groups,
    cutoff = opm_opt("min.mode"), downcase = TRUE, full = TRUE,
    in.parens = FALSE, html = FALSE, sep = " ", ..., exact = TRUE,
    strict = TRUE) 
  ## S4 method for signature 'OPMX'
listing(x, as.groups,
    cutoff = opm_opt("min.mode"), downcase = TRUE, full = TRUE,
    in.parens = FALSE, html = FALSE, sep = " ", ..., exact = TRUE,
    strict = TRUE) 
  ## S4 method for signature 'well_coords_map'
listing(x) 

  ## S4 method for signature 'ANY'
wells(object, full = TRUE, in.parens = FALSE,
    max = opm_opt("max.chars"), brackets = FALSE, clean = TRUE,
    word.wise = FALSE, paren.sep = " ", downcase = FALSE, rm.num = FALSE,
    plate = "PM01", prefix = FALSE, simplify = FALSE) 
  ## S4 method for signature 'MOPMX'
wells(object, ...) 
  ## S4 method for signature 'OPM'
wells(object, full = FALSE, in.parens = TRUE,
    max = opm_opt("max.chars"), brackets = FALSE, clean = TRUE,
    word.wise = FALSE, paren.sep = " ", downcase = FALSE, rm.num = FALSE,
    plate = plate_type(object), prefix = FALSE, simplify = TRUE) 
  ## S4 method for signature 'OPMS'
wells(object, ...) 
  ## S4 method for signature 'missing'
wells(object, ...)

Arguments

object

OPM object, OPMS or MOPMX object or well name or index. If missing, defaults to the selection of all possible wells (for the default plate type, see below).

full

Logical scalar. Return the full names of the wells (if available) or just their coordinates on the plate? The following arguments have no effect if full is FALSE.

in.parens

Logical scalar. If TRUE, add the full name of the substrate in parentheses (or brackets) after the original name. If FALSE, replace by the full substrate name. Note that adding in parentheses (or brackets) is only done if the trimmed substrate names are not empty.

max

Numeric scalar. Maximum number of characters allowed in the names. Longer names are truncated and the truncation is indicated by appending a dot.

brackets

Logical scalar. Use brackets instead of parentheses?

clean

Logical scalar. If TRUE, clean trimmed end of full substrate name from non-word characters; use an empty string if only the dot remained.

word.wise

Logical scalar. If TRUE, abbreviation works by truncating each word separately, and removing vowels first.

paren.sep

Character scalar. What to insert before the opening parenthesis (or bracket) if full is chosen. Currently only zero to many whitespace characters are allowed. The ability to insert a line break is the main purpose of this argument. Using the ‘at sign’ as value is the only alternative and also special, as it causes the plate name itself to be appended to the well coordinate (after an ‘at sign’, without parentheses or brackets). So mapping is not actually done in that case but the resulting names are understood by certain other opm methods which can conduct the mapping at a later stage.

downcase

Logical scalar indicating whether full names should be (carefully) converted to lower case. This uses substrate_info in downcase mode; see there for details.

rm.num

Logical scalar indicating whether numbering (used in the case of replicated substrates per plate) should be stripped from the end of the full well names.

plate

Name of the plate type. Several ones can be given unless object is of class OPM or OPMS. Normalisation as in plate_type is applied before searching for the substrate names but otherwise the match must be exact.

prefix

Logical scalar indicating whether the (short) plate name should be prepended to the well name. Only works in conjunction with full and in.parens.

simplify

Logical scalar indicating whether the result should be simplified to a vector. This will never be done if more than a single column is contained, i.e. if data for more than a single plate type are queried for.

...

Optional arguments passed between the methods.

x

OPMD, OPMS or well_coords_map object.

as.groups

Key suitable for querying the metadata, or NULL. If non-empty, passed as eponymous argument to extract. Thus TRUE and FALSE can be used, creating either a single group or one per plate. The extracted metadata define groups for which the discretised data are aggregated.

If x is an OPMD object and as.groups is not empty, it is used to create the row name of the single row of the resulting OPMS_Listing object. Otherwise an OPMD_Listing object is produced.

cutoff

Numeric scalar used if ‘as.groups’ is non-empty. If the relative frequency of the most frequent entry within the discretised values to be joined is below that cutoff, NA is used. Ignored if x is an OPMD object but added to the result if as.groups is non-empty.

html

Logical scalar. Convert to HTML? This involves Greek letters and paragraph (‘div’) tags.

sep

Character scalar used for joining the ‘as.groups’ entries (if any).

exact

Logical scalar passed to metadata.

strict

Logical scalar also passed to metadata.

Details

Do not confuse wells this with well. The purpose of the OPM and OPMS methods for wells should be obvious. The default method is intended for providing a quick overview of the substrates contained in one to several plates if full is TRUE. If full is FALSE, it can be used to study the effect of the well-index translation and well-name normalisation approaches as used by opm, particularly by the sub-creation methods (see [).

Value

The wells methods return a named character vector or a named matrix of the S3 class well_coords_map, depending on simplify and plate.

The return value of the listing methods for OPMX objects is a character vector or matrix with additional class attribute OPMD_Listing or OPMS_Listing.

The well_coords_map method creates a nested list of the class well_coords_listing which can be used in conjunction with to_yaml or saveRDS for externally storing well maps. See the examples for details.

See Also

base::strtrim base::abbreviate

Other naming-functions: find_positions, find_substrate, gen_iii, opm_files, plate_type, register_plate, select_colors, substrate_info

Examples

## wells() 'OPM' method
(x <- wells(vaas_1, full = FALSE))[1:10]

##  [1] "A01" "A02" "A03" "A04" "A05" "A06" "A07" "A08" "A09" "A10"

(y <- wells(vaas_1, full = TRUE))[1:10]

##                      A01                      A02                      A03 
## "A01 (Negative Control)"          "A02 (Dextrin)"        "A03 (D-Maltose)" 
##                      A04                      A05                      A06 
##      "A04 (D-Trehalose)"     "A05 (D-Cellobiose)"    "A06 (b-Gentiobiose)" 
##                      A07                      A08                      A09 
##          "A07 (Sucrose)"         "A08 (Turanose)"        "A09 (Stachyose)" 
##                      A10 
## "A10 (Positive Control)"

(z <- wells(vaas_1, full = TRUE, in.parens = FALSE))[1:10]

##                A01                A02                A03 
## "Negative Control"          "Dextrin"        "D-Maltose" 
##                A04                A05                A06 
##      "D-Trehalose"     "D-Cellobiose"    "b-Gentiobiose" 
##                A07                A08                A09 
##          "Sucrose"         "Turanose"        "Stachyose" 
##                A10 
## "Positive Control"

# string lengths differ depending on selection
stopifnot(nchar(x) < nchar(y), nchar(z) < nchar(y))

## wells() 'OPM' method
(xx <- wells(vaas_4, full = FALSE))[1:10]

##  [1] "A01" "A02" "A03" "A04" "A05" "A06" "A07" "A08" "A09" "A10"

# wells are guaranteed to be uniform within OPMS objects
stopifnot(identical(x, xx))

## wells() default method
x <- c("A01", "B10")
(y <- wells(x, plate = "PM1"))

##     PM01              
## A01 "Negative Control"
## B10 "Sodium Formate"  
## attr(,"class")
## [1] "well_coords_map"

stopifnot(nchar(y) > nchar(x))
(z <- wells(x, plate = "PM1", in.parens = TRUE))

##     PM01                    
## A01 "A01 (Negative Control)"
## B10 "B10 (Sodium Formate)"  
## attr(,"class")
## [1] "well_coords_map"

stopifnot(nchar(z) > nchar(y))
# formula yields same result
stopifnot(y == wells(~ c(A01, B10), plate = "PM1"))
# querying for several plate types at once
(y <- wells(~ c(A01, B10), plate = c("PM2", "PM3", "PM10")))

##     PM02               PM03               PM10                   
## A01 "Negative Control" "Negative Control" "pH 3.5"               
## B10 "m-Erythritol"     "L-Serine"         "L-Isoleucine + pH 4.5"
## attr(,"class")
## [1] "well_coords_map"

stopifnot(dim(y) == c(2, 3))
(z <- listing(y)) # create a printable nested list

## PM02:
## - Carbon Sources
## - A01: Negative Control
##   B10: m-Erythritol
## PM03:
## - Nitrogen Sources
## - A01: Negative Control
##   B10: L-Serine
## PM10:
## - pH
## - A01: pH 3.5
##   B10: L-Isoleucine + pH 4.5

stopifnot(is.list(z), sapply(z, is.list), names(z) == colnames(y))
# using a sequence of well coordinates
stopifnot(nrow(wells(~ C02:C06)) == 5) # well sequence
stopifnot(nrow(wells(plate = "PM1")) == 96) # all wells by default

## listing() 'OPMD' method

# this yields one sentence for each kind of reaction:
(x <- listing(vaas_1, NULL))

## Positive              Positive for dextrin, D-maltose,
##                       D-trehalose, beta-gentiobiose, positive
##                       control, pH 6, pH 5, alpha-D-lactose,
##                       D-melibiose, beta-methyl-D-glucoside,
##                       N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, 1% NaCl, 4% NaCl,
##                       8% NaCl, D-glucose, D-mannose, D-fructose,
##                       D-galactose, L-fucose, L-rhamnose, inosine,
##                       1% sodium lactate, fusidic acid, D-serine
##                       #2, D-sorbitol, D-mannitol, glycerol,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid,
##                       vancomycin, tetrazolium violet, tetrazolium
##                       blue, L-lactic acid, alpha-keto-glutaric
##                       acid, D-malic acid, L-malic acid,
##                       bromo-succinic acid, lithium chloride,
##                       beta-hydroxy-butyric acid, propionic acid,
##                       acetic acid, aztreonam, butyric acid and
##                       sodium bromate.
## Negative              Negative for negative control, D-arabitol,
##                       gelatin, L-histidine, L-pyroglutamic acid,
##                       pectin, glucuronamide, mucic acid, quinic
##                       acid, D-saccharic acid,
##                       p-hydroxy-phenylacetic acid, D-lactic acid
##                       methyl ester, citric acid, tween 40,
##                       gamma-amino-n-butyric acid and acetoacetic
##                       acid.
## Ambiguous             Ambiguous for D-cellobiose, sucrose,
##                       turanose, stachyose, D-raffinose, D-salicin,
##                       3-O-methyl-D-glucose, D-fucose,
##                       myo-inositol, D-aspartic acid, L-arginine,
##                       L-glutamic acid, methyl pyruvate, nalidixic
##                       acid, potassium tellurite,
##                       alpha-hydroxy-butyric acid,
##                       alpha-keto-butyric acid and sodium formate.

stopifnot(inherits(x, "OPMD_Listing"), is.character(x), length(x) == 3,
  !is.null(names(x)))

# create an 'OPMS_Listing' object
(y <- listing(vaas_1, ~ Species + Strain))

## Escherichia coli DSM30083T
## --------------------------
## Positive              Positive for dextrin, D-maltose,
##                       D-trehalose, beta-gentiobiose, positive
##                       control, pH 6, pH 5, alpha-D-lactose,
##                       D-melibiose, beta-methyl-D-glucoside,
##                       N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, 1% NaCl, 4% NaCl,
##                       8% NaCl, D-glucose, D-mannose, D-fructose,
##                       D-galactose, L-fucose, L-rhamnose, inosine,
##                       1% sodium lactate, fusidic acid, D-serine
##                       #2, D-sorbitol, D-mannitol, glycerol,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid,
##                       vancomycin, tetrazolium violet, tetrazolium
##                       blue, L-lactic acid, alpha-keto-glutaric
##                       acid, D-malic acid, L-malic acid,
##                       bromo-succinic acid, lithium chloride,
##                       beta-hydroxy-butyric acid, propionic acid,
##                       acetic acid, aztreonam, butyric acid and
##                       sodium bromate.
## Negative              Negative for negative control, D-arabitol,
##                       gelatin, L-histidine, L-pyroglutamic acid,
##                       pectin, glucuronamide, mucic acid, quinic
##                       acid, D-saccharic acid,
##                       p-hydroxy-phenylacetic acid, D-lactic acid
##                       methyl ester, citric acid, tween 40,
##                       gamma-amino-n-butyric acid and acetoacetic
##                       acid.
## Ambiguous             Ambiguous for D-cellobiose, sucrose,
##                       turanose, stachyose, D-raffinose, D-salicin,
##                       3-O-methyl-D-glucose, D-fucose,
##                       myo-inositol, D-aspartic acid, L-arginine,
##                       L-glutamic acid, methyl pyruvate, nalidixic
##                       acid, potassium tellurite,
##                       alpha-hydroxy-butyric acid,
##                       alpha-keto-butyric acid and sodium formate.

stopifnot(inherits(y, "OPMS_Listing"), is.matrix(y), dim(y) == c(1, 3),
  y == x, colnames(y) == names(x), !is.null(rownames(y)))

# including HTML tags
(y <- listing(vaas_1, NULL, html = TRUE))

## Positive              <div>Positive for dextrin,
##                       <small>D</small>-maltose,
##                       <small>D</small>-trehalose,
##                       &beta;-gentiobiose, positive control, pH 6,
##                       pH 5, &alpha;-<small>D</small>-lactose,
##                       <small>D</small>-melibiose,
##                       &beta;-methyl-<small>D</small>-glucoside,
##                       <i>N</i>-acetyl-<small>D</small>-glucosamine,
##                       <i>N</i>-acetyl-&beta;-<small>D</small>-mannosamine,
##                       <i>N</i>-acetyl-<small>D</small>-galactosamine,
##                       <i>N</i>-acetyl-neuraminic acid, 1% NaCl, 4%
##                       NaCl, 8% NaCl, <small>D</small>-glucose,
##                       <small>D</small>-mannose,
##                       <small>D</small>-fructose,
##                       <small>D</small>-galactose,
##                       <small>L</small>-fucose,
##                       <small>L</small>-rhamnose, inosine, 1%
##                       sodium lactate, fusidic acid,
##                       <small>D</small>-serine #2,
##                       <small>D</small>-sorbitol,
##                       <small>D</small>-mannitol, glycerol,
##                       <small>D</small>-glucose-6-phosphate,
##                       <small>D</small>-fructose-6-phosphate,
##                       <small>D</small>-serine #1, troleandomycin,
##                       rifamycin SV, minocycline, gly-pro,
##                       <small>L</small>-alanine,
##                       <small>L</small>-aspartic acid,
##                       <small>L</small>-serine, lincomycin,
##                       guanidine hydrochloride, niaproof,
##                       <small>D</small>-galacturonic acid,
##                       <small>L</small>-galactonic
##                       acid-&gamma;-lactone,
##                       <small>D</small>-gluconic acid,
##                       <small>D</small>-glucuronic acid,
##                       vancomycin, tetrazolium violet, tetrazolium
##                       blue, <small>L</small>-lactic acid,
##                       &alpha;-keto-glutaric acid,
##                       <small>D</small>-malic acid,
##                       <small>L</small>-malic acid, bromo-succinic
##                       acid, lithium chloride,
##                       &beta;-hydroxy-butyric acid, propionic acid,
##                       acetic acid, aztreonam, butyric acid and
##                       sodium bromate.</div>
## Negative              <div>Negative for negative control,
##                       <small>D</small>-arabitol, gelatin,
##                       <small>L</small>-histidine,
##                       <small>L</small>-pyroglutamic acid, pectin,
##                       glucuronamide, mucic acid, quinic acid,
##                       <small>D</small>-saccharic acid,
##                       <i>p</i>-hydroxy-phenylacetic acid,
##                       <small>D</small>-lactic acid methyl ester,
##                       citric acid, tween 40,
##                       &gamma;-amino-n-butyric acid and acetoacetic
##                       acid.</div>
## Ambiguous             <div>Ambiguous for
##                       <small>D</small>-cellobiose, sucrose,
##                       turanose, stachyose,
##                       <small>D</small>-raffinose,
##                       <small>D</small>-salicin,
##                       3-<i>O</i>-methyl-<small>D</small>-glucose,
##                       <small>D</small>-fucose, myo-inositol,
##                       <small>D</small>-aspartic acid,
##                       <small>L</small>-arginine,
##                       <small>L</small>-glutamic acid, methyl
##                       pyruvate, nalidixic acid, potassium
##                       tellurite, &alpha;-hydroxy-butyric acid,
##                       &alpha;-keto-butyric acid and sodium
##                       formate.</div>

stopifnot(inherits(y, "OPMD_Listing"), is.character(x), nchar(y) > nchar(x),
  !is.null(names(x)))

## listing() 'OPMS' method

# no grouping, no names (numbering used instead for row names)
(x <- listing(vaas_4[1:2], as.groups = NULL))

## 1
## -
## Positive              Positive for positive control, pH 6, pH 5,
##                       1% NaCl, 4% NaCl, 8% NaCl, 1% sodium
##                       lactate, fusidic acid,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid, mucic
##                       acid, D-saccharic acid, vancomycin,
##                       tetrazolium violet, tetrazolium blue,
##                       L-lactic acid, alpha-keto-glutaric acid,
##                       D-malic acid, L-malic acid,
##                       alpha-hydroxy-butyric acid, acetic acid,
##                       aztreonam and butyric acid.
## Negative              Negative for negative control, D-maltose,
##                       D-trehalose, D-cellobiose, beta-gentiobiose,
##                       sucrose, turanose, stachyose, D-raffinose,
##                       alpha-D-lactose, D-melibiose,
##                       beta-methyl-D-glucoside, D-salicin,
##                       N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, D-glucose,
##                       D-mannose, D-fructose, D-galactose,
##                       3-O-methyl-D-glucose, D-fucose, L-fucose,
##                       D-mannitol, D-arabitol, myo-inositol,
##                       glycerol, D-aspartic acid, gelatin,
##                       L-arginine, L-glutamic acid, L-histidine,
##                       L-pyroglutamic acid, pectin, glucuronamide,
##                       quinic acid, p-hydroxy-phenylacetic acid,
##                       D-lactic acid methyl ester, citric acid,
##                       bromo-succinic acid, nalidixic acid,
##                       potassium tellurite, tween 40,
##                       gamma-amino-n-butyric acid,
##                       beta-hydroxy-butyric acid, acetoacetic acid
##                       and sodium formate.
## Ambiguous             Ambiguous for dextrin, L-rhamnose, inosine,
##                       D-serine #2, D-sorbitol, methyl pyruvate,
##                       lithium chloride, alpha-keto-butyric acid,
##                       propionic acid and sodium bromate.
## 
## 2
## -
## Positive              Positive for dextrin, D-maltose,
##                       D-trehalose, beta-gentiobiose, positive
##                       control, pH 6, pH 5, alpha-D-lactose,
##                       D-melibiose, beta-methyl-D-glucoside,
##                       N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, 1% NaCl, 4% NaCl,
##                       8% NaCl, D-glucose, D-mannose, D-fructose,
##                       D-galactose, L-fucose, L-rhamnose, inosine,
##                       1% sodium lactate, fusidic acid, D-serine
##                       #2, D-sorbitol, D-mannitol, glycerol,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid,
##                       vancomycin, tetrazolium violet, tetrazolium
##                       blue, L-lactic acid, alpha-keto-glutaric
##                       acid, D-malic acid, L-malic acid,
##                       bromo-succinic acid, lithium chloride,
##                       alpha-hydroxy-butyric acid,
##                       beta-hydroxy-butyric acid, propionic acid,
##                       acetic acid, aztreonam, butyric acid and
##                       sodium bromate.
## Negative              Negative for D-arabitol, gelatin,
##                       L-histidine, pectin, mucic acid, quinic
##                       acid, D-saccharic acid,
##                       p-hydroxy-phenylacetic acid, D-lactic acid
##                       methyl ester, citric acid, tween 40,
##                       gamma-amino-n-butyric acid and acetoacetic
##                       acid.
## Ambiguous             Ambiguous for negative control,
##                       D-cellobiose, sucrose, turanose, stachyose,
##                       D-raffinose, D-salicin,
##                       3-O-methyl-D-glucose, D-fucose,
##                       myo-inositol, D-aspartic acid, L-arginine,
##                       L-glutamic acid, L-pyroglutamic acid,
##                       glucuronamide, methyl pyruvate, nalidixic
##                       acid, potassium tellurite,
##                       alpha-keto-butyric acid and sodium formate.

stopifnot(inherits(x, "OPMS_Listing"), is.matrix(x), dim(x) == c(2, 3))
stopifnot(!is.null(rownames(x)), !is.null(colnames(x)))
(y <- listing(vaas_4[1:2], as.groups = FALSE)) # alternative

## 1
## -
## Positive              Positive for positive control, pH 6, pH 5,
##                       1% NaCl, 4% NaCl, 8% NaCl, 1% sodium
##                       lactate, fusidic acid,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid, mucic
##                       acid, D-saccharic acid, vancomycin,
##                       tetrazolium violet, tetrazolium blue,
##                       L-lactic acid, alpha-keto-glutaric acid,
##                       D-malic acid, L-malic acid,
##                       alpha-hydroxy-butyric acid, acetic acid,
##                       aztreonam and butyric acid.
## Negative              Negative for negative control, D-maltose,
##                       D-trehalose, D-cellobiose, beta-gentiobiose,
##                       sucrose, turanose, stachyose, D-raffinose,
##                       alpha-D-lactose, D-melibiose,
##                       beta-methyl-D-glucoside, D-salicin,
##                       N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, D-glucose,
##                       D-mannose, D-fructose, D-galactose,
##                       3-O-methyl-D-glucose, D-fucose, L-fucose,
##                       D-mannitol, D-arabitol, myo-inositol,
##                       glycerol, D-aspartic acid, gelatin,
##                       L-arginine, L-glutamic acid, L-histidine,
##                       L-pyroglutamic acid, pectin, glucuronamide,
##                       quinic acid, p-hydroxy-phenylacetic acid,
##                       D-lactic acid methyl ester, citric acid,
##                       bromo-succinic acid, nalidixic acid,
##                       potassium tellurite, tween 40,
##                       gamma-amino-n-butyric acid,
##                       beta-hydroxy-butyric acid, acetoacetic acid
##                       and sodium formate.
## Ambiguous             Ambiguous for dextrin, L-rhamnose, inosine,
##                       D-serine #2, D-sorbitol, methyl pyruvate,
##                       lithium chloride, alpha-keto-butyric acid,
##                       propionic acid and sodium bromate.
## 
## 2
## -
## Positive              Positive for dextrin, D-maltose,
##                       D-trehalose, beta-gentiobiose, positive
##                       control, pH 6, pH 5, alpha-D-lactose,
##                       D-melibiose, beta-methyl-D-glucoside,
##                       N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, 1% NaCl, 4% NaCl,
##                       8% NaCl, D-glucose, D-mannose, D-fructose,
##                       D-galactose, L-fucose, L-rhamnose, inosine,
##                       1% sodium lactate, fusidic acid, D-serine
##                       #2, D-sorbitol, D-mannitol, glycerol,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid,
##                       vancomycin, tetrazolium violet, tetrazolium
##                       blue, L-lactic acid, alpha-keto-glutaric
##                       acid, D-malic acid, L-malic acid,
##                       bromo-succinic acid, lithium chloride,
##                       alpha-hydroxy-butyric acid,
##                       beta-hydroxy-butyric acid, propionic acid,
##                       acetic acid, aztreonam, butyric acid and
##                       sodium bromate.
## Negative              Negative for D-arabitol, gelatin,
##                       L-histidine, pectin, mucic acid, quinic
##                       acid, D-saccharic acid,
##                       p-hydroxy-phenylacetic acid, D-lactic acid
##                       methyl ester, citric acid, tween 40,
##                       gamma-amino-n-butyric acid and acetoacetic
##                       acid.
## Ambiguous             Ambiguous for negative control,
##                       D-cellobiose, sucrose, turanose, stachyose,
##                       D-raffinose, D-salicin,
##                       3-O-methyl-D-glucose, D-fucose,
##                       myo-inositol, D-aspartic acid, L-arginine,
##                       L-glutamic acid, L-pyroglutamic acid,
##                       glucuronamide, methyl pyruvate, nalidixic
##                       acid, potassium tellurite,
##                       alpha-keto-butyric acid and sodium formate.

stopifnot(identical(x, y))

# in effect no grouping, but names
(x <- listing(vaas_4[1:2], as.groups = list("Species", "Strain")))

## Escherichia coli DSM18039
## -------------------------
## Positive              Positive for positive control, pH 6, pH 5,
##                       1% NaCl, 4% NaCl, 8% NaCl, 1% sodium
##                       lactate, fusidic acid,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid, mucic
##                       acid, D-saccharic acid, vancomycin,
##                       tetrazolium violet, tetrazolium blue,
##                       L-lactic acid, alpha-keto-glutaric acid,
##                       D-malic acid, L-malic acid,
##                       alpha-hydroxy-butyric acid, acetic acid,
##                       aztreonam and butyric acid.
## Negative              Negative for negative control, D-maltose,
##                       D-trehalose, D-cellobiose, beta-gentiobiose,
##                       sucrose, turanose, stachyose, D-raffinose,
##                       alpha-D-lactose, D-melibiose,
##                       beta-methyl-D-glucoside, D-salicin,
##                       N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, D-glucose,
##                       D-mannose, D-fructose, D-galactose,
##                       3-O-methyl-D-glucose, D-fucose, L-fucose,
##                       D-mannitol, D-arabitol, myo-inositol,
##                       glycerol, D-aspartic acid, gelatin,
##                       L-arginine, L-glutamic acid, L-histidine,
##                       L-pyroglutamic acid, pectin, glucuronamide,
##                       quinic acid, p-hydroxy-phenylacetic acid,
##                       D-lactic acid methyl ester, citric acid,
##                       bromo-succinic acid, nalidixic acid,
##                       potassium tellurite, tween 40,
##                       gamma-amino-n-butyric acid,
##                       beta-hydroxy-butyric acid, acetoacetic acid
##                       and sodium formate.
## Ambiguous             Ambiguous for dextrin, L-rhamnose, inosine,
##                       D-serine #2, D-sorbitol, methyl pyruvate,
##                       lithium chloride, alpha-keto-butyric acid,
##                       propionic acid and sodium bromate.
## 
## Escherichia coli DSM30083T
## --------------------------
## Positive              Positive for dextrin, D-maltose,
##                       D-trehalose, beta-gentiobiose, positive
##                       control, pH 6, pH 5, alpha-D-lactose,
##                       D-melibiose, beta-methyl-D-glucoside,
##                       N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, 1% NaCl, 4% NaCl,
##                       8% NaCl, D-glucose, D-mannose, D-fructose,
##                       D-galactose, L-fucose, L-rhamnose, inosine,
##                       1% sodium lactate, fusidic acid, D-serine
##                       #2, D-sorbitol, D-mannitol, glycerol,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid,
##                       vancomycin, tetrazolium violet, tetrazolium
##                       blue, L-lactic acid, alpha-keto-glutaric
##                       acid, D-malic acid, L-malic acid,
##                       bromo-succinic acid, lithium chloride,
##                       alpha-hydroxy-butyric acid,
##                       beta-hydroxy-butyric acid, propionic acid,
##                       acetic acid, aztreonam, butyric acid and
##                       sodium bromate.
## Negative              Negative for D-arabitol, gelatin,
##                       L-histidine, pectin, mucic acid, quinic
##                       acid, D-saccharic acid,
##                       p-hydroxy-phenylacetic acid, D-lactic acid
##                       methyl ester, citric acid, tween 40,
##                       gamma-amino-n-butyric acid and acetoacetic
##                       acid.
## Ambiguous             Ambiguous for negative control,
##                       D-cellobiose, sucrose, turanose, stachyose,
##                       D-raffinose, D-salicin,
##                       3-O-methyl-D-glucose, D-fucose,
##                       myo-inositol, D-aspartic acid, L-arginine,
##                       L-glutamic acid, L-pyroglutamic acid,
##                       glucuronamide, methyl pyruvate, nalidixic
##                       acid, potassium tellurite,
##                       alpha-keto-butyric acid and sodium formate.

stopifnot(inherits(x, "OPMS_Listing"), is.matrix(x), dim(x) == c(2, 3))
stopifnot(!is.null(rownames(x)), !is.null(colnames(x)))

# only single group for all plates
(y <- listing(vaas_4[1:2], as.groups = TRUE))

## 1
## -
## Positive              Positive for positive control, pH 6, pH 5,
##                       1% NaCl, 4% NaCl, 8% NaCl, 1% sodium
##                       lactate, fusidic acid,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid,
##                       vancomycin, tetrazolium violet, tetrazolium
##                       blue, L-lactic acid, alpha-keto-glutaric
##                       acid, D-malic acid, L-malic acid,
##                       alpha-hydroxy-butyric acid, acetic acid,
##                       aztreonam and butyric acid.
## Negative              Negative for D-arabitol, gelatin,
##                       L-histidine, pectin, quinic acid,
##                       p-hydroxy-phenylacetic acid, D-lactic acid
##                       methyl ester, citric acid, tween 40,
##                       gamma-amino-n-butyric acid and acetoacetic
##                       acid.
## Ambiguous             Ambiguous for negative control, dextrin,
##                       D-maltose, D-trehalose, D-cellobiose,
##                       beta-gentiobiose, sucrose, turanose,
##                       stachyose, D-raffinose, alpha-D-lactose,
##                       D-melibiose, beta-methyl-D-glucoside,
##                       D-salicin, N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, D-glucose,
##                       D-mannose, D-fructose, D-galactose,
##                       3-O-methyl-D-glucose, D-fucose, L-fucose,
##                       L-rhamnose, inosine, D-serine #2,
##                       D-sorbitol, D-mannitol, myo-inositol,
##                       glycerol, D-aspartic acid, L-arginine,
##                       L-glutamic acid, L-pyroglutamic acid,
##                       glucuronamide, mucic acid, D-saccharic acid,
##                       methyl pyruvate, bromo-succinic acid,
##                       nalidixic acid, lithium chloride, potassium
##                       tellurite, beta-hydroxy-butyric acid,
##                       alpha-keto-butyric acid, propionic acid,
##                       sodium formate and sodium bromate.

stopifnot(inherits(y, "OPMS_Listing"), is.matrix(y), dim(y) == c(1, 3))
stopifnot(!is.null(rownames(x)), !is.null(colnames(x)))

# two groups
(x <- listing(vaas_4, as.groups = list("Species")))

## Escherichia coli
## ----------------
## Positive              Positive for positive control, pH 6, pH 5,
##                       1% NaCl, 4% NaCl, 8% NaCl, 1% sodium
##                       lactate, fusidic acid,
##                       D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-serine #1,
##                       troleandomycin, rifamycin SV, minocycline,
##                       gly-pro, L-alanine, L-aspartic acid,
##                       L-serine, lincomycin, guanidine
##                       hydrochloride, niaproof, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-gluconic acid, D-glucuronic acid,
##                       vancomycin, tetrazolium violet, tetrazolium
##                       blue, L-lactic acid, alpha-keto-glutaric
##                       acid, D-malic acid, L-malic acid,
##                       alpha-hydroxy-butyric acid, acetic acid,
##                       aztreonam and butyric acid.
## Negative              Negative for D-arabitol, gelatin,
##                       L-histidine, pectin, quinic acid,
##                       p-hydroxy-phenylacetic acid, D-lactic acid
##                       methyl ester, citric acid, tween 40,
##                       gamma-amino-n-butyric acid and acetoacetic
##                       acid.
## Ambiguous             Ambiguous for negative control, dextrin,
##                       D-maltose, D-trehalose, D-cellobiose,
##                       beta-gentiobiose, sucrose, turanose,
##                       stachyose, D-raffinose, alpha-D-lactose,
##                       D-melibiose, beta-methyl-D-glucoside,
##                       D-salicin, N-acetyl-D-glucosamine,
##                       N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, D-glucose,
##                       D-mannose, D-fructose, D-galactose,
##                       3-O-methyl-D-glucose, D-fucose, L-fucose,
##                       L-rhamnose, inosine, D-serine #2,
##                       D-sorbitol, D-mannitol, myo-inositol,
##                       glycerol, D-aspartic acid, L-arginine,
##                       L-glutamic acid, L-pyroglutamic acid,
##                       glucuronamide, mucic acid, D-saccharic acid,
##                       methyl pyruvate, bromo-succinic acid,
##                       nalidixic acid, lithium chloride, potassium
##                       tellurite, beta-hydroxy-butyric acid,
##                       alpha-keto-butyric acid, propionic acid,
##                       sodium formate and sodium bromate.
## 
## Pseudomonas aeruginosa
## ----------------------
## Positive              Positive for positive control, pH 6, pH 5,
##                       1% NaCl, 4% NaCl, 8% NaCl, 1% sodium
##                       lactate, fusidic acid, troleandomycin,
##                       rifamycin SV, minocycline, gly-pro,
##                       L-alanine, L-arginine, L-aspartic acid,
##                       L-glutamic acid, L-histidine, L-pyroglutamic
##                       acid, lincomycin, guanidine hydrochloride,
##                       niaproof, D-gluconic acid, quinic acid,
##                       vancomycin, tetrazolium violet, tetrazolium
##                       blue, p-hydroxy-phenylacetic acid, L-lactic
##                       acid, citric acid, alpha-keto-glutaric acid,
##                       L-malic acid, nalidixic acid, potassium
##                       tellurite, gamma-amino-n-butyric acid,
##                       beta-hydroxy-butyric acid, propionic acid,
##                       acetic acid, aztreonam and butyric acid.
## Negative              Negative for negative control, dextrin,
##                       D-maltose, D-trehalose, D-cellobiose,
##                       beta-gentiobiose, sucrose, turanose,
##                       stachyose, D-raffinose, alpha-D-lactose,
##                       D-melibiose, beta-methyl-D-glucoside,
##                       D-salicin, N-acetyl-beta-D-mannosamine,
##                       N-acetyl-D-galactosamine,
##                       N-acetyl-neuraminic acid, D-mannose,
##                       D-galactose, 3-O-methyl-D-glucose, D-fucose,
##                       L-fucose, L-rhamnose, D-sorbitol,
##                       myo-inositol, D-glucose-6-phosphate,
##                       D-fructose-6-phosphate, D-aspartic acid,
##                       D-serine #1, gelatin, pectin, D-galacturonic
##                       acid, L-galactonic acid-gamma-lactone,
##                       D-glucuronic acid, glucuronamide, mucic
##                       acid, D-saccharic acid, methyl pyruvate,
##                       D-lactic acid methyl ester, D-malic acid,
##                       bromo-succinic acid, alpha-hydroxy-butyric
##                       acid, alpha-keto-butyric acid and
##                       acetoacetic acid.
## Ambiguous             Ambiguous for N-acetyl-D-glucosamine,
##                       D-glucose, D-fructose, inosine, D-serine #2,
##                       D-mannitol, D-arabitol, glycerol, L-serine,
##                       lithium chloride, tween 40, sodium formate
##                       and sodium bromate.

stopifnot(inherits(x, "OPMS_Listing"), is.matrix(x), dim(x) == c(2, 3))
stopifnot(!is.null(rownames(x)), !is.null(colnames(x)))
[Package opm version 1.3.63 Index]