U mdp @sddlmZmZddlZddlZddlmZddlm Z ddl m Z ddl m Z dd l mZdd lmZdd l mZmZd ZeeZdeeeeedfeeeeeee eeeeeeed ddZdS))UnionOptionalN)AnnData)spmatrix)_utils)logging)get_init_pos_from_paga)Literal) AnyRandom _choose_graph)frdrlkkgrid_frZlglrtZ rt_circularfarF) adatalayoutinit_posroot random_staten_jobs adjacency key_added_ext neighbors_keyobspcopyc Ks<td|} |tkr(tdtd| r4|n|}|dkrLt|| |}||jkrf|j|} nB|dksr|rt||||| d} n"t j |t j |j ddf} |d krzdd l m}Wn"tk rtd d }YnX|d krV|d d d ddddd dd dd d }d| kr"| d}nd| kr6| d}nd}|j|| |d}t |}nt |t|}|dkr|j|fd| i| }n@d|kr|dk r|g}|j|fd|i| }n|j|f| }t |j}i|jd<t||d|jdd<d|p|}||j|<tjd| d |d!d"| r8|SdS)#a Force-directed graph drawing [Islam11]_ [Jacomy14]_ [Chippada18]_. An alternative to tSNE that often preserves the topology of the data better. This requires to run :func:`~scanpy.pp.neighbors`, first. The default layout ('fa', `ForceAtlas2`) [Jacomy14]_ uses the package |fa2|_ [Chippada18]_, which can be installed via `pip install fa2`. `Force-directed graph drawing`_ describes a class of long-established algorithms for visualizing graphs. It has been suggested for visualizing single-cell data by [Islam11]_. Many other layouts as implemented in igraph [Csardi06]_ are available. Similar approaches have been used by [Zunder15]_ or [Weinreb17]_. .. |fa2| replace:: `fa2` .. _fa2: https://github.com/bhargavchippada/forceatlas2 .. _Force-directed graph drawing: https://en.wikipedia.org/wiki/Force-directed_graph_drawing Parameters ---------- adata Annotated data matrix. layout 'fa' (`ForceAtlas2`) or any valid `igraph layout `__. Of particular interest are 'fr' (Fruchterman Reingold), 'grid_fr' (Grid Fruchterman Reingold, faster than 'fr'), 'kk' (Kamadi Kawai', slower than 'fr'), 'lgl' (Large Graph, very fast), 'drl' (Distributed Recursive Layout, pretty fast) and 'rt' (Reingold Tilford tree layout). root Root for tree layouts. random_state For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If `None`, no seed is set. adjacency Sparse adjacency matrix of the graph, defaults to neighbors connectivities. key_added_ext By default, append `layout`. proceed Continue computation, starting off with 'X_draw_graph_`layout`'. init_pos `'paga'`/`True`, `None`/`False`, or any valid 2d-`.obsm` key. Use precomputed coordinates for initialization. If `False`/`None` (the default), initialize randomly. neighbors_key If not specified, draw_graph looks .obsp['connectivities'] for connectivities (default storage place for pp.neighbors). If specified, draw_graph looks .obsp[.uns[neighbors_key]['connectivities_key']] for connectivities. obsp Use .obsp[obsp] as adjacency. You can't specify both `obsp` and `neighbors_key` at the same time. copy Return a copy instead of writing to adata. **kwds Parameters of chosen igraph layout. See e.g. `fruchterman-reingold`_ [Fruchterman91]_. One of the most important ones is `maxiter`. .. _fruchterman-reingold: http://igraph.org/python/doc/igraph.Graph-class.html#layout_fruchterman_reingold Returns ------- Depending on `copy`, returns or updates `adata` with the following field. **X_draw_graph_layout** : `adata.obsm` Coordinates of graph layout. E.g. for layout='fa' (the default), the field is called 'X_draw_graph_fa' z'drawing single-cell graph using layout zProvide a valid layout, one of .NZpaga)rrrrrr) ForceAtlas2zPackage 'fa2' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2' (`pip install fa2`).rFg?Tg333333?g@) ZoutboundAttractionDistributionZ linLogModeZ adjustSizesZedgeWeightInfluenceZjitterToleranceZbarnesHutOptimizeZbarnesHutThetaZ multiThreadedZ scalingRatioZstrongGravityModeZgravityverbosemaxiter iterationsi)posr#>rrrrseedrr draw_graph)rrparamsZ X_draw_graph_z finishedz added z(, graph_drawing coordinates (adata.obsm))timedeep)logginfo_LAYOUTS ValueErrorrr Zobsmkeysr nprandomr%shapeZfa2r ImportErrorwarning forceatlas2arrayrZget_igraph_from_adjacencyrtolistZcoordsZunsdict)rrrrrrrrrrrkwdsstartZ init_coordsr r4r#Z positionsgZ ig_layoutZ key_addedr;Q/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/scanpy/tools/_draw_graph.pyr&sS                    r&) rNNrNNNNNF)typingrrnumpyr/r0ZanndatarZ scipy.sparserrrr*r Z_compatr r r r,Z_Layoutstrboolintr&r;r;r;r<sD