How do I generate a matrix? - ruby

Question

I have the following data:
gene strain
A1 S1
A1 S4
A1 S8
A2 S5
A2 S4
A2 S9
A3 S4
A3 S1
A3 S10
I need to produce a matrix that has the genes vs strains, I.E., I need to show which genes are present in which strains, so the matrix will look like this:
S1 S4 S5 S8 S9 S10
A1
A2
A3
Can anyone guide me through the best and quickest way to do this in Ruby? I have the array of strains and genes.

Answer 1

There are many ways you could represent the gene-strain matrix you need. The best way will depend on what you want to do with the matrix. Do you want to compare which strains are present in different genes? Or compare which genes have a given strain? Do you just want to be able to look up whether a given gene has a given strain?
One simple way would be a Hash whose keys are Sets:
require 'set'
h = Hash.new { |h,k| h[k] = Set.new }
# assuming you already have the data in an array of arrays...
data.each do |gene,strain|
h[gene] << strain
end
If you only want to print a matrix out on the screen, here is a little script to do so:
require 'set'
genes, strains = Set.new, Set.new
h = Hash.new { |h,k| h[k] = Set.new }
# again assuming you already have the data in an array of arrays
data.each { |g,s| h[g] << s; genes << g; strains << s }
genes, strains = genes.sort, strains.sort
FIELD_WIDTH = 5
BLANK = " "*FIELD_WIDTH
X = "X" + (" " * (FIELD_WIDTH - 1))
def print_fixed_width(str)
str = str[0,FIELD_WIDTH]
print str
print " "*(FIELD_WIDTH-str.length)
end
# now print the matrix
print BLANK
strains.each { |s| print_fixed_width(s) }
puts
genes.each do |g|
print_fixed_width(g)
strains.each { |s| h[g].include?(s) ? print X : print BLANK }
puts
end
Please post more details on what you want to do with the matrix and I will provide a more appropriate option if necessary.

Answer 2

You can represent this in a 2d array:
arr = [[1,1],[1,4],[1,8],[2,5],[2,4],[2,9],[3,4],[3,1],[3,10]]
quick and dirty table:
s = " 1234567890\n"
(1..3).each do |i|
s << i.to_s << ' '
(1..10).each do |j|
s << ( arr.include?( [i,j] ) ? 'x' : ' ' )
end
s << "\n"
end
puts s
1234567890
1 x x x
2 xx x
3 x x x

Answer 3

If you " need to check which genes are present in which strains", then a Hash would be sufficient:
str = <<DOC
A1 S1
A1 S4
A1 S8
A2 S5
A2 S4
A2 S9
A3 S4
A3 S1
A3 S10
DOC
ar = str.lines.map{|line| line.split(/\s+/) } #string to array of arrays
genes_from_strain = Hash.new{|h,k| h[k]=[] } #This hash will give an empty array if key is not present
ar.each{|pair| genes_from_strain[pair.last] << pair.first }
p genes_from_strain['S1'] #=>["A1", "A3"]