Manipulate.jl

PopGenCore.jl/src/Manipulate.jl

📦 not exported	🟪 exported by PopGenCore.jl	🔵 exported by PopGen.jl

🟪🔵 sampleinfo!

sampleinfo!(::PopData, metadata::Pair{Symbol, Vector}; categorical::Bool = false)
sampleinfo!(::PopData, metadata::Pair{String, Vector}; categorical::Bool = false)

Add an additional sample information to PopData metadata. Mutates PopData in place. Metadata must be in the same order as the samples in sampleinfo(popdata).

Arguments

metadata : A Pair of :ColumnName => [Values]

Keyword Arguments

categorical : Boolean of whether the metadata being added is categorical aka "factors" (default: false) Example

cats = @nancycats
sampleinfo!(cats, :whiskerlength => rand(cats.metadata.samples))
sampleinfo!(cats, "tailcolor" => rand(["orange", "brown"], metadata(cats).samples), categorical = true)
cats
PopData{Diploid, 9 Microsatellite loci}
  Samples: 237
  Populations: 17
  Other Info: ["whiskerlength", "tailcolor"]

🟪🔵 locusinfo!

locusinfo!(::PopData, metadata::Pair{Symbol, Vector}; categorical::Bool = false)
locusinfo!(::PopData, metadata::Pair{String, Vector}; categorical::Bool = false)

Add an additional locus information to PopData metadata. Mutates PopData in place. Metadata must be in the same order as the samples in locusinfo(PopData).

Arguments

metadata : A Pair of :ColumnName => [Values]

Keyword Arguments

categorical : Boolean of whether the metadata being added is categorical aka "factors" (default: false) Example

cats = @nancycats
locusinfo!(cats, :quality => rand(metadata(cats).loci))
cats
PopData{Diploid, 9 Microsatellite loci}
  Samples: 237
  Populations: 17
  Other Info: ["quality"]

🟪🔵 locationdata!

locationdata!(data::PopData; longitude::Vector{Float64}, latitude::Vector{Float64})

Replaces existing PopData geographic coordinate data. Takes decimal degrees as a Vector of any AbstractFloat.

Formatting requirements

Decimal Degrees format: -11.431
Must use negative sign - instead of cardinal directions
Location data must be in the order that samples appear in your PopData
Missing data should be coded as missing values of type Missing (can be accomplished with replace!())

Example

ncats = @nancycats ;
x = rand(237) ; y = rand(237)
locationdata!(ncats, longitude = x, latitude = y)

locationdata!(data::PopData; longitude::Vector{String}, latitude::Vector{String})

Replaces existing PopData geographic coordinate data. Takes decimal minutes or degrees minutes seconds format as a Vector of String. Recommended to use CSV.read from CSV.jl to import your spatial coordinates from a text file.

Formatting requirements

Coordinates as a String separated by spaces ("11 43 41") or colons ("11:43:41")
Must use negative sign ("-11 43.52") or single-letter cardinal direction ("11 43.52W")
Missing data should be coded as the string "missing" (can be accomplished with replace!())
Can mix colons and spaces (although it's bad practice)

NOTE

If you read in the coordinate data as 4 vectors (longitude degrees, longitude minutes, latitude degrees, latitude minutes), then the easiest course of action would be to merge them into two vectors of strings (one for longitude, one for latitude):

long_string = string.(lat_deg, " ", lat_min)
lat_string = string.(long_deg, " ", long_min)

and use these as inputs into locations!

Example

ncats = @nancycats;
x = fill("11 22.33W", 237) ; y = fill("-41 31.52", 237)
locationdata!(ncats, longitude = x, latitude = y)

locationdata!(data::PopData, longitude::Vector{String}, latitude::Vector{String})
locationdata!(data::PopData; kwargs...)

🟪🔵 populations!

# Replace by matching
populations!(data::PopData, rename::Dict)
populations!(data::PopData, rename::Vector{String})
populations!(data::PopData, samples::Vector{String}, populations::Vector{String})

Multiple methods to rename or reassign population names to a PopData.

Rename using a Dictionary

Rename existing population ID's of PopData using a Dict of population_name => replacement

Example

potatopops = Dict("1" => "Idaho", "2" => "Russet")
populations!(potatoes, potatopops)

Rename using a Vector of Strings

If the number of new names is equal to the number of current unique population names, the method will rename the existing populations in the order with which they appear via unique(). If the number of new population names is equal to the number of samples, the method will instead assign new population names to every sample in the order with which they appear in sampleinfo(popdata).

Example

# rename (2) existing populations
potatopops = ["Idaho", "Russet"]
populations!(potatoes, potatopops)
# assign new names to all [44] samples
potatopops = repeat(["Idaho", "Russet"], inner = 22) ;
populations!(potatoes, potatopops)

Reassign using samples and new population assignments

Completely reassign populations for each individual. Takes two vectors of strings as input: one of the sample names, and the other with their new corresponding population name. This can be useful to change population names for only some individuals.

Example

populations!(potatoes, ["potato_1", "potato_2"], ["north", "south"])

🟪🔵 exclude!

exclude!(data::PopData, kwargs...)

Edit a PopData object in-place by excluding all occurences of the specified information. The keywords can be used in any combination. Synonymous with omit! and remove!. All values are converted to String for filtering, so Symbol and numbers will also work. This can be considered a simpler and more rudimentary syntax for subsetting or filtering PopData.

Keyword Arguments

`locus`

A String or Vector{String} of loci you want to remove from the PopData. The keyword loci also works.

`population`

A String or Vector{String} of populations you want to remove from the PopData The keyword populations also works.

`name`

A String or Vector{String} of samples you want to remove from the PopData The keywords names, sample, and samples also work.

Examples

cats = @nancycats;
exclude!(cats, name = "N100", population = 1:5)
exclude!(cats, name = ["N100", "N102", "N211"], locus = ["fca8", "fca23"])
exclude!(cats, name = "N102", locus = :fca8, population = "3")

const omit! = exclude!
const remove! = exclude!

🟪🔵 exclude

exclude(data::PopData, kwargs...)

Returns a new PopData object excluding all occurrences of the specified keywords. The keywords can be used in any combination. Synonymous with omit and remove. All values are converted to String for filtering, so Symbol and numbers will also work. This can be considered a simpler and more rudimentary syntax for subsetting or filtering PopData.

Keyword Arguments

`locus`

A String or Vector{String} of loci you want to remove from the PopData.

`population`

A String or Vector{String} of populations you want to remove from the PopData.

`name`

A String or Vector{String} of samples you want to remove from the PopData.

Examples

cats = @nancycats;
exclude(cats, name = "N100", population = 1:5)
exclude(cats, name = ["N100", "N102", "N211"], locus = ["fca8", "fca23"])
exclude(cats, name = "N102", locus = :fca8, population = "3")

const omit = exclude
const remove = exclude

🟪🔵 keep!

keep!(data::PopData, kwargs...)

Edit a PopData object in-place by keeping only the occurrences of the specified keywords. If using multiple fields, they will be chained together as "or" statements. All values are converted to String for filtering, so Symbol and numbers will also work. This can be considered a simpler and more rudimentary syntax for subsetting or filtering PopData.

Keyword Arguments

`locus`

A String or Vector{String} of loci you want to keep in the PopData.

`population`

A String or Vector{String} of populations you want to keep in the PopData.

`name`

A String or Vector{String} of samples you want to keep in the PopData.

Examples

cats = @nancycats;
keep!(cats, population = 1:5)
# keep 4 populations and 3 specific samples
keep!(cats, name = ["N100", "N102", "N211"])
# keep 2 loci, 2 populations, and 10 specific individuals
keep!(cats, locus = [:fca8, "fca37"], population = [7,8], name = samplenames(cats)[1:10])

🟪🔵 keep

keep(data::PopData, kwargs...)

Returns a new PopData object keeping only the occurrences of the specified keyword. Unlike exclude(). only one keyword can be used at a time. All values are converted to String for filtering, so Symbol and numbers will also work. This can be considered a simpler and more rudimentary syntax for subsetting or filtering PopData.

Keyword Arguments

`locus`

A String or Vector{String} of loci you want to keep in the PopData.

`population`

A String or Vector{String} of populations you want to keep in the PopData.

`name`

A String or Vector{String} of samples you want to keep in the PopData.

Examples

cats = @nancycats;
keep(cats, population = 1:5)
# equivalent to cats[cats.genodata.population .∈ Ref(string.(1:5)), :]
keep(cats, name = ["N100", "N102", "N211"])
# equivalent to cats[cats.genodata.name .∈ Ref(["N100", "N102", "N211"]), :]
keep(cats, locus = [:fca8, "fca37"])
# equivalent to cats[cats.genodata.locus .∈ Ref(["fca8", "fca37"]), :]

🟪🔵 filter

filter(data::PopData, args...)

A drop-in replacement for DataFrames.filter where PopData is the first argument and the filtering conditions are the second argument. Returns a new PopData. Note the argument order is opposite of that from DataFrames.jl. Example

x = @nancycats ;
y = filter(x, :name => i -> i ∈ samplenames(x)[1:10]) ;
show(x)
PopData{Diploid, 9 Microsatellite loci}
  Samples: 237
  Populations: 17
show(y)
PopData{Diploid, 9 Microsatellite loci}
  Samples: 10
  Populations: 1

🟪🔵 filter!

filter!(data::PopData, args...)

A drop-in replacement for the DataFrames.filter! where PopData is the first argument and the filtering conditions are the second argument. Mutates the PopData in place and returns it. Note the argument order is opposite of that from DataFrames.jl.

Example

x = @nancycats ;
filter!(x, :name => i -> i ∈ samplenames(x)[1:10]) ;
show(x)
PopData{Diploid, 9 Microsatellite loci}
  Samples: 10
  Populations: 1

PopGenCore.jl/src/Manipulate.jl​

🟪🔵 sampleinfo!​

Arguments​

Keyword Arguments​

🟪🔵 locusinfo!​

Arguments​

Keyword Arguments​

🟪🔵 locationdata!​

Formatting requirements​

Formatting requirements​

NOTE​

🟪🔵 populations!​

Rename using a Dictionary​

Rename using a Vector of Strings​

Reassign using samples and new population assignments​

🟪🔵 exclude!​

Keyword Arguments​

locus​

population​

name​

🟪🔵 exclude​

Keyword Arguments​

locus​

population​

name​

🟪🔵 keep!​

Keyword Arguments​

locus​

population​

name​

🟪🔵 keep​

Keyword Arguments​

locus​

population​

name​

🟪🔵 filter​

🟪🔵 filter!​

PopGenCore.jl/src/Manipulate.jl

🟪🔵 sampleinfo!

Arguments

Keyword Arguments

🟪🔵 locusinfo!

Arguments

Keyword Arguments

🟪🔵 locationdata!

Formatting requirements

Formatting requirements

NOTE

🟪🔵 populations!

Rename using a Dictionary

Rename using a Vector of Strings

Reassign using samples and new population assignments

🟪🔵 exclude!

Keyword Arguments

`locus`

`population`

`name`

🟪🔵 exclude

Keyword Arguments

`locus`

`population`

`name`

🟪🔵 keep!

Keyword Arguments

`locus`

`population`

`name`

🟪🔵 keep

Keyword Arguments

`locus`

`population`

`name`

🟪🔵 filter

🟪🔵 filter!