Merge pull request #204 from LCSB-BioCore/develop

Develop→master merge for v0.7.0

Project.toml

@@ -1,31 +1,28 @@
 name = "GigaSOM"
 uuid = "a03a9c34-069e-5582-a11c-5c984cab887c"
-version = "0.6.8"
+version = "0.7.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 DistributedArrays = "aaf54ef3-cdf8-58ed-94cc-d582ad619b94"
+DistributedData = "f6a0035f-c5ac-4ad0-b410-ad102ced35df"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 FCSFiles = "d76558cf-badf-52d4-a17e-381ab0b0d937"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
 
 [compat]
-CSV = "^0.5.12, 0.6, 0.7, 0.8"
+CSV = "^0.5.12, 0.6, 0.7, 0.8, 0.10"
 DataFrames = "0.20, 0.21, 0.22, 1.0"
 Distances = "^0.8.2, 0.9, 0.10"
 DistributedArrays = "^0.6.4"
+DistributedData = "0.1.4, 0.2"
 Distributions = "^0.21.1, 0.22, 0.23, 0.24, 0.25"
 FCSFiles = "^0.1.1"
 FileIO = "^1.0.7"
@@ -36,4 +33,11 @@ XLSX = "^0.5.5, 0.6, 0.7"
 julia = "1"
 
 [extras]
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0"
+
+[targets]
+test = ["JSON", "LinearAlgebra", "SHA", "Test", "XLSX"]

docs/src/functions.md

@@ -27,10 +27,3 @@ Pages = ["core.jl", "trainutils.jl"]
 Modules = [GigaSOM]
 Pages = ["embedding.jl"]
 ```
-
-## Distributed processing tools
-
-```@autodocs
-Modules = [GigaSOM]
-Pages = ["distributed.jl", "dio.jl"]
-```

docs/src/tutorials/basicUsage.md

@@ -33,18 +33,17 @@ While all functions work well on simple data matrices, the main aim of GigaSOM
 is to let the users enjoy the cluster-computing resources. All functions also
 work on data that are "scattered" among workers (i.e. each worker only holds a
 portion of the data loaded in the memory). This dataset description is stored
-in [`LoadedDataInfo`](@ref) structure. Most of the functions above in fact
-accept the `LoadedDataInfo` as argument, and often return another
-`LoadedDataInfo` that describes the scattered result.
+in [`Dinfo`](@ref) structure. Most of the functions above in fact
+accept the `Dinfo` as argument, and often return another
+`Dinfo` that describes the scattered result.
 
-Most importantly, using `LoadedDataInfo` **prevents memory exhaustion at the
+Most importantly, using `Dinfo` **prevents memory exhaustion at the
 master node**, which is a critical feature required to handle huge datasets.
 
 You can always collect the scattered data back into a matrix (if it fits to
-your RAM) with [`distributed_collect`](@ref), and utilize many other functions
-to manipulate it, including e.g. [`distributed_mapreduce`](@ref) for easily
-running parallel computations, or [`distributed_export`](@ref) for saving and
-restoring the dataset paralelly.
+your RAM) with `gather_array`, and utilize many other functions to manipulate
+it, including e.g. `dmapreduce` for easily running parallel computations, or
+`dstore` for saving and restoring the dataset paralelly.
 
 ## Minimal working example
 

docs/src/tutorials/distributedProcessing.md

@@ -13,29 +13,31 @@ aforementioned `dselect` and `dtransform_asinh`. The following code extracts
 means and standard deviations from the first 3 columns of a dataset distributed
 as `di`:
 ```julia
+using DistributedData
+
 dstat(di, [1,2,3])
 ```
 
-## Manual work with the distributed data
+## Manual work with the DistributedData.jl package
 
 We will first show how to use the general framework to compute per-cluster
-statistics. GigaSOM exports the [`distributed_mapreduce`](@ref) function that
+statistics. DistributedData.jl exports the [`dmapreduce`](@ref) function that
 can be used as a very effective basic building block for running such
 computations. For example, you can efficiently compute a distributed mean of
 all your data as such:
 ```julia
-distributed_mapreduce(di, sum, +) / distributed_mapreduce(di, length, +)
+dmapreduce(di, sum, +) / dmapreduce(di, length, +)
 ```
 
-The parameters of `distributed_mapreduce` are, in order:
+The parameters of `dmapreduce` are, in order:
 
 - `di`, the dataset
 - `sum` or `length`, an unary "map" function -- during the computation, each
   piece of distributed data is first _paralelly_ processed by this function
 - `+`, a binary "reduction" or "folding" function -- the pieces of information
   processed by the map function are successively joined in pairs using this
   function, until there is only a single result left. This final result is also
-  what `distributed_mapreduce` returns.
+  what `dmapreduce` returns.
 
 Above example thus reads: Sum all data on all workers, add up the intermediate
 results, and divide the final number to the sum of all lengths of data on the
@@ -45,7 +47,7 @@ Column-wise mean (as produced by `dstat`) is slightly more useful; we only need
 to split the computation on columns:
 
 ```julia
-distributed_mapreduce(di, d -> mapslices(sum, d, dims=1), +) ./ distributed_mapreduce(di, x->size(x,1), +)
+dmapreduce(di, d -> mapslices(sum, d, dims=1), +) ./ dmapreduce(di, x->size(x,1), +)
 ```
 
 Finally, for distributed computation of per-cluster mean, the clustering
@@ -55,7 +57,7 @@ the distributed `mapToGigaSOM` does exactly that).
 First, compute the clustering:
 ```julia
 mapping = mapToGigaSOM(som, di)
-distributed_transform(mapping, m -> metaClusters[m])
+dtransform(mapping, m -> metaClusters[m])
 ```
 
 Now, the distributed computation is run on 2 scattered datasets. We employ a
@@ -66,7 +68,7 @@ following code produces a matrix of tuples `(sum, count)`, for separate
 clusters (in rows) and data columns (in columns):
 
 ```julia
-sumscounts = distributed_mapreduce([di, mapping],
+sumscounts = dmapreduce([di, mapping],
     (d, mapping) -> catmapbuckets(
         (_,clData) -> (sum(clData), length(clData)),
 	d, 10, mapping),
@@ -113,13 +115,13 @@ capture all of the actual 16 existing clusters)
 
 Finally, we can remove the temporary data from workers to create free memory for other analyses:
 ```julia
-undistribute(mapping)
+unscatter(mapping)
 ```
 
 ## Convenience statistical functions
 
 Notably, several of the most used statistical functions are available in
-GigaSOM.jl in a form that can cope with distributed data.
+DistributedData.jl in a form that can cope with distributed data.
 
 For example, you can run a distributed median computation as such:
 ```julia

docs/src/tutorials/processingFCSData.md

@@ -108,7 +108,7 @@ If you are sure you have enough RAM, you can collect the data to the master
 node. (In case of the relatively small Levine13 dataset, you very probably have
 the required 2.5MB of RAM, but there are many larger datasets.)
 ```julia
-e = distributed_collect(e)
+e = gather_array(e)
 ```
 
 ```
@@ -260,13 +260,13 @@ The `metaClusters` represent membership of the SOM codes in cluster; these can
 be expanded to membership of all cells using [`mapToGigaSOM`](@ref):
 
 ```julia
-mapping = distributed_collect(mapToGigaSOM(som, di), free=true)
+mapping = gather_array(mapToGigaSOM(som, di), free=true)
 clusters = metaClusters[mapping]
 ```
 
 `clusters` now contain an integer from `1` to `10` with a classification of
 each cell in the dataset.
 
-(The argument `free=true` of `distributed_collect` automatically removes the
+(The argument `free=true` of `gather_array` automatically removes the
 distributed data from workers after collecting, which saves their memory for
 other datasets.)

src/GigaSOM.jl

@@ -10,6 +10,7 @@ using CSV
 using DataFrames
 using Distances
 using Distributed
+using DistributedData
 using Distributions
 using FCSFiles
 using FileIO
@@ -21,20 +22,15 @@ using StableRNGs
 include("base/structs.jl")
 
 include("base/dataops.jl")
-include("base/distributed.jl")
 include("base/trainutils.jl")
 
 include("analysis/core.jl")
 include("analysis/embedding.jl")
 
-include("io/dio.jl")
 include("io/input.jl")
 include("io/process.jl")
 include("io/splitting.jl")
 
-# include visualization files
-# include("visualization/plotting.jl")
-
 #core
 export initGigaSOM, trainGigaSOM, mapToGigaSOM
 
@@ -45,7 +41,7 @@ export linearRadius, expRadius, gaussianKernel, bubbleKernel, thresholdKernel, d
 export embedGigaSOM
 
 # structs
-export Som, LoadedDataInfo
+export Som
 
 #io/input
 export readFlowset,
@@ -69,40 +65,7 @@ export slicesof, vcollectSlice, collectSlice
 #io/process
 export cleanNames!, getMetaData, getMarkerNames
 
-# plotting
-export plotCounts, plotPCA
-
 #dataops (higher-level operations on data)
-export dcopy,
-    dselect,
-    dapply_cols,
-    dapply_rows,
-    dstat,
-    dstat_buckets,
-    dcount,
-    dcount_buckets,
-    dscale,
-    dtransform_asinh,
-    dmedian,
-    dmedian_buckets,
-    mapbuckets,
-    catmapbuckets
-
-#distributed data tools
-export save_at,
-    get_from,
-    get_val_from,
-    remove_from,
-    distribute_array,
-    distribute_darray,
-    undistribute,
-    distributed_transform,
-    distributed_mapreduce,
-    distributed_foreach,
-    distributed_collect,
-    distributed_export,
-    distributed_import,
-    distributed_unlink
-
+export dtransform_asinh
 
 end # module