Compare attributes of candidate against all pathways requirements.

output.txt

Pathways-attributes matrix
   A B C
p0 0 0 0
p1 0 0 1
p2 0 1 0
p3 1 0 0
p4 0 1 1
p5 1 0 1
p6 1 1 0
p7 1 1 1

Pathways row sums
p0 p1 p2 p3 p4 p5 p6 p7 
 0  1  1  1  2  2  2  3 

candidate 1:
A B C 
0 0 1 
acceptable by paths:
p0 p1

candidate 2:
A B C 
1 0 1 
acceptable by paths:
p0 p1 p3 p5

candidate 3:
A B C 
1 1 1 
acceptable by paths:
p0 p1 p2 p3 p4 p5 p6 p7

path_attr_compare.R

# Each pathway described by attributes, A,B,C
#   Create pathway for every combination of attributes
attr_names <- LETTERS[1:3]
paths <- c(0,0,0, #p0 (no requirements pathway)
           0,0,1, #p1
           0,1,0, #p2
           1,0,0, #p3
           0,1,1, #p4
           1,0,1, #p5
           1,1,0, #p6
           1,1,1) #p7 (full requirements pathway)

# Create matrix and label nicely.
paths_matrix <- matrix(paths, ncol=3, byrow=T)
colnames(paths_matrix) = attr_names
rownames(paths_matrix) = paste('p',0:7,sep='')

# Calculate row sums of the paths matrix
paths_row_sums <- rowSums(paths_matrix)

# Show matrix and sums
cat("Pathways-attributes matrix\n")
print(paths_matrix) 
cat('\n')
cat("Pathways row sums\n")
print(paths_row_sums) 
cat('\n')

# Check a candidate against a matrix of pathways
#  This is essentially performing bitwise AND of the candidate attributes 
#  against each pathway's attributes.  If all a pathway's requirements are met
#  then the result will have the same number of 1's as the pathway.
# Params:
#  cand, a vector of attributes in the same order as p_mat columns
#  p_mat, a the matrix of pathways where attributes are columns.
#  row_sums, the row sums of p_mat to avoid recomputing them each call
candidate_accepting_paths <- function(cand, p_mat, row_sums){
  candidate_sums <- p_mat %*% cand
  matching_sums <- candidate_sums == paths_row_sums
  # return names of paths that have all requirements satisified
  rownames(p_mat)[matching_sums]
}

# Encode a candidate as a vector of attributes 
candidate_1 <- c(0,0,1)
candidate_2 <- c(1,0,1)
candidate_3 <- c(1,1,1)

# Make candidate's named vectors for pretty printing
names(candidate_1) <- attr_names
names(candidate_2) <- attr_names
names(candidate_3) <- attr_names

# Check which paths are the candidates meets the requirements of
c1_accepted <- candidate_accepting_paths(candidate_1, paths_matrix, paths_row_sums)
c2_accepted <- candidate_accepting_paths(candidate_2, paths_matrix, paths_row_sums)
c3_accepted <- candidate_accepting_paths(candidate_3, paths_matrix, paths_row_sums)

# print results
cat("candidate 1:\n")
print(candidate_1) 
cat("acceptable by paths:\n")
cat(paste(c1_accepted, collapse = ' '))
cat('\n\n')

cat("candidate 2:\n")
print(candidate_2) 
cat("acceptable by paths:\n")
cat(paste(c2_accepted, collapse = ' '))
cat('\n\n')

cat("candidate 3:\n")
print(candidate_3) 
cat("acceptable by paths:\n")
cat(paste(c3_accepted, collapse = ' '))
cat('\n')