U md@+@srddlZddlmZddlmZddlmZddlm Z m Z m Z m Z m Z mZmZddlZddlZddlZddlmZddlmZddlmZmZmZddlmZdd lm Z dd l!m"Z"m#Z#dd l$m%Z%dd l&m'Z'd dl(m)Z)d dl)m*Z*m+Z+m,Z,m-Z-ddl(m)Z.m/Z0ddl1m2Z2ddl3m4Z4d8ddee4de e5e6e-dfe e5e,fdddZ7dddddeife e8efddd Z9dddeiddddd!dddddeid"d#d"ddd$dd%ddddddeidd&dd&ddd&dddf(ee e6e e e8e e e8e5fe ee6fffe e+e e8efe ej:e e5e8e e5dfe e8e e8e e8e8fdfe;e8e e8e e8e e5e8e e5e e8efe6e6e6e e6e e6e5e e8e6e e5e ej:e8edfe;e e8e#fe e e e8efe e;e;e;e;e;e e;e e;e8dfe e e e e e dfd''d(d)Zd/d.dd0dd1ddddd&d&d&dddd&ddddfee e e8e5fe e8e;e e8e e8e#dfe e8e e8e#ffe e e8e5e e8ee e5e e5fe e8e e5e e5e;e;e;e e5e6e-dfe e5e,dfe;e;e;e e;e e;e8dfe e e e d2d3d4Z?d9d6d7Z@dS):N)Path)MappingProxyType)OptionalUnionListSequenceMappingAnyTuple)AnnData)is_categorical_dtype)pyplotrcParamsticker) patheffects)Axes) is_color_likeColormap)issparse)check_random_state)_utils)matrix _IGraphLayout _FontWeight _FontSize)rlogging)settings)LiteralF2don databold皙?pos)r Z3d)adata projectionlegend_fontsizelegend_fontweightc%KsZtjddg|d\}}}}|dkr0|jdd}d}|dkrT|dkrH|n|}d\}}|dkrd|jkrld }n4d |jkr|d }n$d |jkrd }nd|jkrd}nd }ddlm}m}m}|||d|||||||| | | | | |||ddd|dkrx||jddkrj|||}||d|jddd} |dd| f}!t j |!ddg|j dj |j |dd}n|jdd}|d|d}"}#|d|"|d|#d|kr|d}$n|}$| dk r| |d<| dk r| |d<| dk r| |d<t|f|ddd||$|||d||dk r8t|tjd||d |dkrV|SdS)!aa Scatter and PAGA graph side-by-side. Consists in a scatter plot and the abstracted graph. See :func:`~scanpy.pl.paga` for all related parameters. See :func:`~scanpy.pl.paga_path` for visualizing gene changes along paths through the abstracted graph. Additional parameters are as follows. Parameters ---------- adata Annotated data matrix. kwds_scatter Keywords for :func:`~scanpy.pl.scatter`. kwds_paga Keywords for :func:`~scanpy.pl.paga`. Returns ------- A list of :class:`~matplotlib.axes.Axes` if `show` is `False`. r)panels right_marginNpagagroups)r/ZX_draw_graph_faZ draw_graph_faZX_umapZumapZX_tsneZtsneZX_draw_graph_frZ draw_graph_fr) embedding _get_basis_components_to_dimensionsF)axbasiscoloredgesalphar. components legend_locr(r)legend_fontoutline color_mappaletteframeonsizetitleshowsave)r8 dimensionsZ total_dimsxy)columnsindexT)Zobservedr%labelsfontsize fontweight fontoutline)r3r@rAr?rGcolorsr=r% paga_comparer@rA)r setup_axesunsZobsmZ scatterplotsr0r1r2shapepd DataFrameZ obs_namesgroupbyobsmedianZ sort_indexZto_numpyZget_xlimget_ylimZset_xlimZset_ylimpopr-plsuptitlesavefig_or_show)%r&r4r6r5r7r.r8r'r9r(r)r:r;r<r=r>r?r, left_marginr@rAZ title_graphZ groups_graphr%Zpaga_graph_paramsaxs_rYr0r1r2Z_basisZdimscoordsxlimZylimrGr`T/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/scanpy/plotting/_tools/paga.pyrLs4                rL) layout_kwdscsddl}ddl}t|}||} |dkr.d}|dkrjzddlm} Wn"tk rhtdd}YnX|dkr|dkr| |j ddf} n| } | dddddd d dd dddd } d |kr|d } nd|kr|d} nd} | j || | d}ddt |DnV|dkrH||}t||t|j dkr^tdn||dt|}d|krt|}|j|t|tr|n|gdj}n|dkr||j}n|dkr| |j ddf} n(| }|dddfd9<|} z|j|f| dd|j}Wn.tk rJ|j|fd| i|j}YnXddt |Dtdkrtdd<tfd d!t | D}|S)"Nrfrfa) ForceAtlas2zPackage 'fa2' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2' (`pip install fa2`).rF?Tg333333?g@) ZoutboundAttractionDistributionZ linLogModeZ adjustSizesZedgeWeightInfluenceZjitterToleranceZbarnesHutOptimizeZbarnesHutThetaZ multiThreadedZ scalingRatioZstrongGravityModeZgravityverbosemaxiter iterationsi)r%ricSs$i|]\}}||d|d gqSrr*r`.0npr`r`ra sz _compute_pos..eq_treezKThis is a forest and not a single tree. 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Compute a coarse-grained layout of the data. Reuse this by passing `init_pos='paga'` to :func:`~scanpy.tl.umap` or :func:`~scanpy.tl.draw_graph` and obtain embeddings with more meaningful global topology [Wolf19]_. This uses ForceAtlas2 or igraph's layout algorithms for most layouts [Csardi06]_. Parameters ---------- adata Annotated data matrix. threshold Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph. color Gene name or `obs` annotation defining the node colors. Also plots the degree of the abstracted graph when passing {`'degree_dashed'`, `'degree_solid'`}. Can be also used to visualize pie chart at each node in the following form: `{: {: , ...}, ...}`. If the fractions do not sum to 1, a new category called `'rest'` colored grey will be created. labels The node labels. If `None`, this defaults to the group labels stored in the categorical for which :func:`~scanpy.tl.paga` has been computed. pos Two-column array-like storing the x and y coordinates for drawing. Otherwise, path to a `.gdf` file that has been exported from Gephi or a similar graph visualization software. layout Plotting layout that computes positions. `'fa'` stands for “ForceAtlas2”, `'fr'` stands for “Fruchterman-Reingold”, `'rt'` stands for “Reingold-Tilford”, `'eq_tree'` stands for “eqally spaced tree”. All but `'fa'` and `'eq_tree'` are igraph layouts. All other igraph layouts are also permitted. See also parameter `pos` and :func:`~scanpy.tl.draw_graph`. layout_kwds Keywords for the layout. init_pos Two-column array storing the x and y coordinates for initializing the layout. random_state For layouts with random initialization like `'fr'`, change this to use different intial states for the optimization. If `None`, the initial state is not reproducible. root If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is `None` or an empty list, the root vertices are automatically calculated based on topological sorting. transitions Key for `.uns['paga']` that specifies the matrix that stores the arrows, for instance `'transitions_confidence'`. solid_edges Key for `.uns['paga']` that specifies the matrix that stores the edges to be drawn solid black. dashed_edges Key for `.uns['paga']` that specifies the matrix that stores the edges to be drawn dashed grey. If `None`, no dashed edges are drawn. single_component Restrict to largest connected component. fontsize Font size for node labels. fontoutline Width of the white outline around fonts. text_kwds Keywords for :meth:`~matplotlib.axes.Axes.text`. node_size_scale Increase or decrease the size of the nodes. node_size_power The power with which groups sizes influence the radius of the nodes. edge_width_scale Edge with scale in units of `rcParams['lines.linewidth']`. min_edge_width Min width of solid edges. max_edge_width Max width of solid and dashed edges. arrowsize For directed graphs, choose the size of the arrow head head's length and width. See :py:class: `matplotlib.patches.FancyArrowPatch` for attribute `mutation_scale` for more info. export_to_gexf Export to gexf format to be read by graph visualization programs such as Gephi. normalize_to_color Whether to normalize categorical plots to `color` or the underlying grouping. cmap The color map. cax A matplotlib axes object for a potential colorbar. cb_kwds Keyword arguments for :class:`~matplotlib.colorbar.Colorbar`, for instance, `ticks`. add_pos Add the positions to `adata.uns['paga']`. title Provide a title. frameon Draw a frame around the PAGA graph. plot If `False`, do not create the figure, simply compute the layout. save If `True` or a `str`, save the figure. A string is appended to the default filename. Infer the filetype if ending on \{`'.pdf'`, `'.png'`, `'.svg'`\}. ax A matplotlib axes object. Returns ------- If `show==False`, one or more :class:`~matplotlib.axes.Axes` objects. Adds `'pos'` to `adata.uns['paga']` if `add_pos` is `True`. Examples -------- .. plot:: :context: close-figs import scanpy as sc adata = sc.datasets.pbmc3k_processed() sc.tl.paga(adata, groups='louvain') sc.pl.paga(adata) You can increase node and edge sizes by specifying additional arguments. .. plot:: :context: close-figs sc.pl.paga(adata, node_size_scale=10, edge_width_scale=2) Notes ----- When initializing the positions, note that – for some reason – igraph mirrors coordinates along the x axis... that is, you should increase the `maxiter` parameter by 1 if the layout is flipped. .. currentmodule:: scanpy See also -------- tl.paga pl.paga_compare pl.paga_path Nz9`groups` is deprecated in `pl.paga`: use `labels` insteadr-r.cs<t|tjo$t|tjjjk}|p:|dkp:t|tSN)rcabc CollectionrrTcat categoriesstr)rCZhas_one_per_category)r& groups_keyr`rais_flats zpaga..is_flatcSsi|]\}}||qSr`r`)rlirmr`r`raroszpaga..csi|]\}}|||qSr`)get)rlrmv) names_to_ixsr`raros csg|]}qSr`r`rlr]rGr`rar{szpaga..r*cSsg|]}|qSr`r`rlcr`r`rar{scsg|]}qSr`r`r)r?r`rar{scSsg|]}dqSrr`rr`r`rar{scs2g|]*}|kr&j|jjdkp,|kqS)category)obs_keysrTZdtypenamer)r& var_namesr`rar{scSsg|]}dqS)Fr`rr`r`rar{ sz-If `root` is a string, it needs to be one of z not .rcsg|]}t|qSr`)rrF)rlrrr`rar{sr>rrrp rt_circularconnectivities_tree)rrrrbrrs)r3r+ colorbars)rKrrrrradjacency_dashedrsrGrHrIrJrrrrrrrr=rcolorbarrrr?rrrr%g~jtx?r皙?)formatrr%z3added 'pos', the PAGA positions (adata.uns['paga'])rMF))rrrOrrrnextiterrrTrritemsrZ_frameonrangerrrawrrrrFrrdataeliminate_zerosrrrN set_title _paga_graphrXZgcfZadd_axesrrZ FuncFormatterZticks_formatterhintrZ)=r&rr5rrbrrsrGrrrrrHrIrJrrrrrrrr?r[rr%rrrrrr=rrrrKr.rr@rAr3rrrrrr\Z panel_posZdraw_region_widthZ figure_widthZicolorrsctbottomheightwidthleftZ rectangleZfigZax_cbr]r`)r&rrGrr?rrar-sF              !         r- reference)rrcU s ddl}| } | dk rJt| trJ| |jddkrJtd|jdd| |jdd}!| dkrn|j|!jj} dks|!kr|!dk r|!d|jkst |j|!jjt |j|!dkrt ||!|j|!dt |j|!jjD]\}"}#|#t jkrd|"<q||}$|dk r"||}%t|ttfs8|}&nt|}|jdkrTtdd }'|4}(|(|(D] })|)d rq|'|)7}'qnW5QRXdd lm}*tj|*|'d d }+|+ddgj}&ddt |&D}ttrtrfddtt | DttrdrdkrBdd|%jddDn*dkrddd|$jddDntdttt t|j!dkr|j"n|j!j"},ttrJ|,krJg}-|j|!jj}.t |.D]f\}/}0|0|j|!kj}1|j!dk r|r|j!ddf}2n|ddf}2|-#t$|2j%|1q|-ttrƈ|jkrt&|jsg}-|j|!jj}.t |.D]4\}/}0|0|j|!kj}1|-#|jj'|1f$q|-ttr4|jkr4t&|jr4t(j)||!|rdndd\}3}4t |t(*|jd|4}5|5t t | krdtdt | d t d!t+j,j-.|\}6} |6d"kr|st/0d#|6d"kr^|r^t1| }7t2|7|7 kdd}8|3| |8kddf}|4dd| |8kf}t| |8kt| | |8k} |j|!jj| |8k5}9t/6d$|9||}$|dk r^td%|dt7d&}:|dk rd'd|%j8d(d)D};|:t|;};|dk rt9|;d|};|j:|%|||;dd*d+d,|dkrPd-d|$j8d(d)D};|:t|;};|dk s|dk rt9|;||};t;<$t;=d.|j:|$|||;d/d0W5QRXn|jd|>}<|dkrpd1}d|}?t| |>|$jG|>d6<t|>|$jG|>d7<tHtHd8||>dd8||>d"dd9d:|$jG|>d;<q0t jId<}@t/Jd=|@t jIjKd(d(d>|L|$t jId<|M||Ng|Og|!dk r"|!d?|jkr"|j|!d?}AntPt | }Ad@}B|BtQ|jRddA|}CtS|A}D|CtT|A|D|}A| dkrt7dB} | dk rtH|}tUjV| dCdDg|dE<tdtWjX s>t |&}E|jY|&dddf|&ddd"fd|EdF|A|dG}Ft | D]:\}>}G|jZ|&|>df|&|>d"f|GfdHdH| | dI|qnt t[|&dddf|&ddd"fD]\\}H}IttWjX stdJ\}JfdKd|JD}Kt]|K}L|Ld"k rt^|J}J|J#d|K#d"t]|Kn$t_|Ld" stdLdM|Ld!t`|K}M|M|Md }Mdg|M5}Mt[|Mdd |Md"d|JD]\}N}O}PtadNtjb|NdNtjb|OdO}Qdgtc|Q5}Rdgtd|Q5}Ste|R|Sg}Ttf|T }'|jY|Hg|Ig|T|'dN|A|PdP}F qR| dk rd|jZ|H|I| fdHdH| | dI| qd|FS)QNrr-r.z>Provide a list of group labels for the PAGA groups {}, not {}._colorsZgreyz.gdfzqCurrently only supporting reading positions from .gdf files. 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