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authorMuriithi Frederick Muriuki2021-07-23 09:18:40 +0300
committerMuriithi Frederick Muriuki2021-07-23 09:18:40 +0300
commit278f1a18b59b1cadd04c50a9af35b5aece4d722d (patch)
tree7cf307f6fb0443c644fd051e51d65688c3846cf3 /gn3
parent8705e9186051fb5d11d150991c49f6f73056183b (diff)
downloadgenenetwork3-278f1a18b59b1cadd04c50a9af35b5aece4d722d.tar.gz
Add data examples for `slink`. Implement function.
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Copy the function, mostly verbatim from genenetwork1. See: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L107-L138 * tests/unit/computations/test_slink.py: Add a test with some example data to test that the implementation gives the same results as that in genenetwork1
Diffstat (limited to 'gn3')
-rw-r--r--gn3/computations/slink.py48
1 files changed, 47 insertions, 1 deletions
diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py
index 59d0975..8d51f29 100644
--- a/gn3/computations/slink.py
+++ b/gn3/computations/slink.py
@@ -123,9 +123,55 @@ def nearest(lists, i, j):
def slink(lists):
"""
+ DESCRIPTION:
+ TODO: Not quite sure what this function does. Work through the code with a
+ fine tooth comb, once we understand the context of its use, so as to
+ give a better description
+
+ The name of the function does not clearly establish what the function
+ does either, meaning, once that is established, the function should be
+ renamed to give the user an idea of what it does without necessarily
+ reading through a ton of code.
+
+ We should also look into refactoring the function to reduce/eliminate
+ the multiple levels of nested-loops and conditionals
+
+ PARAMETERS:
+ lists (list of lists of numbers): Give this a better name.
+ Each item of this list is a list of coordinates of the members in the
+ group.
+ What 'member' and 'group' in this context means, is not yet established.
"""
try:
- nearest(lists, 1, 2)
+ size = len(lists)
+ listindex = range(size)
+ listindexcopy = list(range(size))
+ listscopy = [[item for item in child] for child in lists]
+ initSize = size
+ candidate = []
+ while initSize >2:
+ mindist = 1e10
+ for i in range(initSize):
+ for j in range(i+1,initSize):
+ if listscopy[i][j] < mindist:
+ mindist = listscopy[i][j]
+ candidate=[[i,j]]
+ elif listscopy[i][j] == mindist:
+ mindist = listscopy[i][j]
+ candidate.append([i,j])
+ else:
+ pass
+ newmem = (listindexcopy[candidate[0][0]],listindexcopy[candidate[0][1]],mindist)
+ listindexcopy.pop(candidate[0][1])
+ listindexcopy[candidate[0][0]] = newmem
+
+ initSize -= 1
+ for i in range(initSize):
+ for j in range(i+1,initSize):
+ listscopy[i][j] = nearest(lists,listindexcopy[i],listindexcopy[j])
+ listscopy[j][i] = listscopy[i][j]
+ listindexcopy.append(nearest(lists,listindexcopy[0],listindexcopy[1]))
+ return listindexcopy
except Exception as e:
# TODO: Look into making the logging log output to the system's
# configured logger(s)