fix a bug in Read.hs

src/IGraph/Internal/Data.chs

@@ -123,6 +123,7 @@ listToStrVector xs = do
 
 {#fun igraph_matrix_ncol as ^ { `MatrixPtr' } -> `Int' #}
 
+-- row lists to matrix
 listsToMatrixPtr :: [[Double]] -> IO MatrixPtr
 listsToMatrixPtr xs = do
     mptr <- igraphMatrixNew r c
@@ -134,11 +135,15 @@ listsToMatrixPtr xs = do
     r = length xs
     c = maximum $ map length xs
 
+-- to row lists
 matrixPtrToLists :: MatrixPtr -> IO [[Double]]
-matrixPtrToLists mptr = do
+matrixPtrToLists = liftM transpose . matrixPtrToColumnLists
+
+matrixPtrToColumnLists :: MatrixPtr -> IO [[Double]]
+matrixPtrToColumnLists mptr = do
     r <- igraphMatrixNrow mptr
     c <- igraphMatrixNcol mptr
     xs <- allocaArray (r*c) $ \ptr -> do
         igraphMatrixCopyTo mptr ptr
         peekArray (r*c) ptr
-    return $ transpose $ chunksOf r $ map realToFrac xs
+    return $ chunksOf r $ map realToFrac xs

src/IGraph/Layout.hs

@@ -27,7 +27,7 @@ kamadaKawai :: Graph d => LGraph d v e -> Double -> Double -> Double -> Double -
 kamadaKawai gr sigma initemp coolexp kkconst opt = unsafePerformIO $ do
     mptr <- mat
     igraphLayoutKamadaKawai (_graph gr) mptr (_nIter opt) sigma initemp coolexp kkconst useSeed nullPtr nullPtr nullPtr nullPtr
-    [x, y] <- matrixPtrToLists mptr
+    [x, y] <- matrixPtrToColumnLists mptr
     return $ zip x y
   where
     (useSeed, mat) = case _seed opt of

src/IGraph/Read.hs

@@ -11,25 +11,25 @@ readAdjMatrix fl = do
     c <- B.readFile fl
     let (header:xs) = B.lines c
         mat = map (map (fst . fromJust . readDouble) . B.words) xs
-        es = fst $ unzip $ filter f $ zip [ (i,j) | i <- [0..nrow-1], j <- [i..nrow-1] ] $ concat mat
+        es = fst $ unzip $ filter f $ zip [ (i,j) | i <- [0..nrow-1], j <- [0..nrow-1] ] $ concat mat
         nrow = length mat
         ncol = length $ head mat
     if nrow /= ncol
        then error "nrow != ncol"
        else return $ mkGraph (nrow, Just $ B.words header) (es, Nothing)
   where
-    f ((i,j),v) = i /= j && v /= 0
+    f ((i,j),v) = i < j && v /= 0
 
 readAdjMatrixWeighted :: Graph d => FilePath -> IO (LGraph d B.ByteString Double)
 readAdjMatrixWeighted fl = do
     c <- B.readFile fl
     let (header:xs) = B.lines c
         mat = map (map (fst . fromJust . readDouble) . B.words) xs
-        (es, ws) = unzip $ filter f $ zip [ (i,j) | i <- [0..nrow-1], j <- [i..nrow-1] ] $ concat mat
+        (es, ws) = unzip $ filter f $ zip [ (i,j) | i <- [0..nrow-1], j <- [0..nrow-1] ] $ concat mat
         nrow = length mat
         ncol = length $ head mat
     if nrow /= ncol
        then error "nrow != ncol"
        else return $ mkGraph (nrow, Just $ B.words header) (es, Just ws)
   where
-    f ((i,j),v) = i /= j && v /= 0
+    f ((i,j),v) = i < j && v /= 0

test.hs

@@ -18,15 +18,11 @@ import System.Environment
 
 main = do
     [fl] <- getArgs
-    g <- readAdjMatrix fl :: IO (LGraph U B.ByteString ())
-    let n = nNodes g
-        r = map (f g) [0..n-1]
-    mapM_ h r
-  where
-    f g i = let name = nodeLab g i
-                xs = map (nodeLab g) $ neighbors g i
-            in (name, B.intercalate "," xs)
-    h (a,b) = do
-        B.putStr a
-        B.putStr "\t"
-        B.putStrLn b
+    g <- readAdjMatrixWeighted fl :: IO (LGraph U B.ByteString Double)
+    let m = _labelToNode g
+        [a] = M.lookupDefault [] "H3K27ac" m
+        [b] = M.lookupDefault [] "H3K4me1" m
+        ws = Just $ map (abs . edgeLabByEid g) [0 .. nEdges g - 1]
+        cs = (map.map) (nodeLab g) $ communityLeadingEigenvector g ws 10000
+    print $ edgeLab g (b,a)
+    mapM_ print cs