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Edit labels

Source: R/editLabels.R
editLabels.Rd

Function for editing node labels, i.e., shortening to a certain length and removing unwanted characters.

The function is used by NetCoMi's plot functions plot.microNetProps and plot.diffnet.

Usage

editLabels(
  x,
  shortenLabels = c("intelligent", "simple", "none"),
  labelLength = 6,
  labelPattern = NULL,
  addBrack = TRUE,
  charToRm = NULL,
  verbose = TRUE
)

Arguments

x

character vector with node labels.

shortenLabels

character indicating how to shorten the labels. Available options are:

"intelligent"

Elements of charToRm are removed, labels are shortened to length labelLength, and duplicates are removed using labelPattern.

"simple"

Elements of charToRm are removed and labels are shortened to length labelLength.

"none"

Labels are not shortened.

labelLength

integer defining the length to which labels shall be shortened if shortenLabels is used. Defaults to 6.

labelPattern

vector of three or five elements, which is used if argument shortenLabels is set to "intelligent". If cutting a label to length labelLength leads to duplicates, the label is shortened according to labelPattern, where the first entry gives the length of the first part, the second entry is used a separator, and the third entry is the length of the third part. If labelPattern has five elements and the shortened labels are still not unique, the fourth element serves as further separator, and the fifth element gives the length of the last label part. Defaults to c(4, "'", 3, "'", 3). See details for an example.

addBrack

logical indicating whether to add a closing square bracket. If TRUE, a "]" is added if the first part contains a "[".

charToRm

character vector giving one or more patterns to remove from the labels.

verbose

logical. If TRUE, the function is allowed to return messages.

Value

Character vector with edited labels.

Details

Consider a vector with three bacteria names: "Streptococcus1", "Streptococcus2", and "Streptomyces".

shortenLabels = "simple" with labelLength = 6 leads to shortened labels: "Strept", "Strept", and "Strept", which are not distinguishable.

shortenLabels = "intelligent" with labelPattern = c(5, "'", 3) leads to shortened labels: "Strep'coc", "Strep'coc", are "Strep'myc", where the first two are not distinguishable.

shortenLabels = "intelligent" with labelPattern = c(5, "'", 3, "'", 3) leads to shortened labels: "Strep'coc'1", "Strep'coc'2", and "Strep'myc", from which the original labels can be inferred.

The intelligent approach is as follows:

First, labels are shortened to the defined length (argument labelLength). The labelPattern is then applied to all duplicated labels. For each group of duplicates, the third label part starts at the letter where two or more labels are different for the first time. The five-part pattern (if given) applies if a group of duplicates consists of more than two labels and if the shortened labels are not unique after applying the three-part pattern. Then, the fifth part starts at the letter where all labels are different for the first time.

A message is printed if the returned labels are not unique.

Examples

labels <- c("Salmonella", 
            "Clostridium", "Clostridiales(O)", 
            "Ruminococcus", "Ruminococcaceae(F)", 
            "Enterobacteriaceae", "Enterococcaceae",
            "[Bacillus] alkalinitrilicus",
            "[Bacillus] alkalisediminis",
            "[Bacillus] oceani")

# Use the "simple" method to shorten labels
editLabels(labels, shortenLabels = "simple", labelLength = 6)
#>  [1] "Salmon" "Clostr" "Clostr" "Rumino" "Rumino" "Entero" "Entero" "[Bacil"
#>  [9] "[Bacil" "[Bacil"
# -> Original labels cannot be inferred from shortened labels

# Use the "intelligent" method to shorten labels with three-part pattern
editLabels(labels, shortenLabels = "intelligent", labelLength = 6,
           labelPattern = c(6, "'", 4))
#> Shortened labels could not be made unique.
#>  [1] "Salmon"       "Clostr'um  "  "Clostr'ales"  "Rumino'us  "  "Rumino'acea" 
#>  [6] "Entero'bact"  "Entero'cocc"  "[Bacil]'alka" "[Bacil]'alka" "[Bacil]'ocea"
# -> [Bacillus] alkalinitrilicus and [Bacillus] alkalisediminis not 
#    distinguishable

# Use the "intelligent" method to shorten labels with five-part pattern
editLabels(labels, shortenLabels = "intelligent", labelLength = 6,
           labelPattern = c(6, "'", 3, "'", 3))
#>  [1] "Salmon"          "Clostr'um "      "Clostr'ale"      "Rumino'us "     
#>  [5] "Rumino'ace"      "Entero'bac"      "Entero'coc"      "[Bacil]'alk'nit"
#>  [9] "[Bacil]'alk'sed" "[Bacil]'oce"    

# Same as before but no brackets are added
editLabels(labels, shortenLabels = "intelligent", labelLength = 6, 
           addBrack = FALSE, labelPattern = c(6, "'", 3, "'", 3))
#>  [1] "Salmon"         "Clostr'um "     "Clostr'ale"     "Rumino'us "    
#>  [5] "Rumino'ace"     "Entero'bac"     "Entero'coc"     "[Bacil'alk'nit"
#>  [9] "[Bacil'alk'sed" "[Bacil'oce"    

# Remove character pattern(s) (can also be a vector with multiple patterns)
labels <- c("g__Faecalibacterium", "g__Clostridium", "g__Eubacterium", 
            "g__Bifidobacterium", "g__Bacteroides")
            
editLabels(labels, charToRm = "g__")
#> [1] "Faecal" "Clostr" "Eubact" "Bifido" "Bacter"