o RŀgT@sVdZddlZddlZddlmZddZdddZdd d Zed d dddfd dZ dS)zUtilities for handling, displaying and exporting Phylo trees. Third-party libraries are loaded when the corresponding function is called. N)MissingPythonDependencyErrorcszddl}Wn tytddw|jdkrddn|jdkr'ddnd dfd d |jr:|}n|}||j||j|S) a.Convert a Tree object to a networkx graph. The result is useful for graph-oriented analysis, and also interactive plotting with pylab, matplotlib or pygraphviz, though the resulting diagram is usually not ideal for displaying a phylogeny. Requires NetworkX version 0.99 or later. rNz0Install NetworkX if you want to use to_networkx.z1.0cSs|j|||jpddt|dr!|jdur!|j|||d<nt|dr:|jdur:|j|||d<|j|_t|drO|jdurO|j|||d<dSt|drh|jdurj|j|||d<|j|_dSdSdS)N?)weightcolorwidth)add_edge branch_lengthhasattrrto_hexrgraphn1n2rD/var/www/html/myenv/lib/python3.10/site-packages/Bio/Phylo/_utils.pyr*s zto_networkx..add_edgez0.99cSs||||jpddS)Nr)rrr rrrr=scSs|||dSN)rr rrrrBscs4|D]}||j||j|j||qdS)z5Walk down the Tree, building graphs, edges and nodes.N)add_noderoot)r topcladerbuild_subgraphrrrEs   z#to_networkx..build_subgraph) networkx ImportErrorr __version__rootedDiGraphGraphrr)treerGrrr to_networkxs*        r rrc szddl}Wn tytddw|jdkrtdtdd|Ddkr/|Sfdd g}|dur>d }d d |D}d d |D}|jdd||||D] }t||dkre||=qX|D] }t||dkru||=qh|j|||t |j d}|S)aConvert a Tree object to an igraph Graph. The result is useful for graph-oriented analysis and interactive plotting with matplotlib, Cairo, and plotly. Requires python-igraph version 0.10.0 or later. :Parameters: vertex_attributes : sequence of strings A sequence of strings containing the Clade properties that are to be stored as vertex attributes, e.g. "name". edge_attributes : sequence of strings A sequence of strings containing the Clade properties that are to be stored as edge attributes, e.g. "color" and "width". In both cases, if a property is not found it will be ignored. rNz,Install igraph if you want to use to_igraph.z0.10ztszto_igraph..c s|D]}t||r!t||dkrdg||<t|||||<qd}t|D])\}} |d|} |d7}||| f|D]}t| |rP||t| |q?q(|} ||}t|D]\}} | d|} | | ||||}q\|S)z*Add edges from this subtree, breath-first.rNr")r lengetattr enumerateappend) noden_nodecounteredges edge_attrs vertex_attrsattrname delta_counterichildn_child old_counter add_subtreen_nodesrrr8|s0     zto_igraph..add_subtreercSi|]}|gqSrrr$r1rrr zto_igraph..cSr:rrr;rrrr<r=)r.r0r/directed) igraphrrrsum find_cladesrrr'boolr) rvertex_attributesedge_attributesigr.r/r0r1r rr7r to_igraphUsL   &rFPc s|durtj}|tddD}||ddtd}fdd}fdd }||||fd d t|Dfd d |jdtD]$\}}d| } |ddkrr| dt |d7} | | dqU| ddS)aDraw an ascii-art phylogram of the given tree. The printed result looks like:: _________ Orange ______________| | |______________ Tangerine ______________| | | _________________________ Grapefruit _| |_________| | |______________ Pummelo | |__________________________________ Apple :Parameters: file : file-like object File handle opened for writing the output drawing. (Default: standard output) column_width : int Total number of text columns used by the drawing. Ncss|] }tt|VqdSr)r'str)r$taxonrrrr&szdraw_ascii..r"csh|}t|dkr|jdd}ttttd}|t|fdd|DS)z6Create a mapping of each clade to its column position.rTunit_branch_lengthsrJcs"i|] \}}|t|dqS)r)int)r$rblencols_per_branch_unitrrr<sz9draw_ascii..get_col_positions..) depthsmaxvaluesrMmathceillogr'items)rrQ fudge_margin) drawing_widthtaxarOrget_col_positionss  z%draw_ascii..get_col_positionscs.ddtDfdd|jS)NcSsi|] \}}|d|qS)rJr)r$idxrIrrrr<sz9draw_ascii..get_row_positions..csB|D] }|vr |q|jd|jdd|<dS)NrrJcladesrsubcladecalc_row positionsrrrcs z7draw_ascii..get_row_positions..calc_row)r)rr)rZrbrget_row_positionss z%draw_ascii..get_row_positionscsg|] }ddtDqS)cSsg|]}dqS) rr#rrr sz)draw_ascii...)range)r$y)rYrrrhszdraw_ascii..c s|}|}t||D]}d||<q |jrV|jd}|jd}t|d|dD]}d||<q0|jd|dkrJd||<|D] }||dqLdSdS)N_rr]r"|rJ,)rir_) rstartcolthiscolthisrowcoltoprowbotrowrowr4) char_matrix col_positions draw_clade row_positionsrrrws  zdraw_ascii..draw_claderrg ) sysstdout get_terminalsrRr'rirr)joinrstriprHwrite) rfile column_widthmax_label_widthdrawing_heightr[rfr\rtliner)rurvrwrYrxrZr draw_asciis&    rTc szddlm Wnty$zddl Wn ty!tddwYnwddlm gg ddsC|r>fddnddnttrOfd dn t sWt d rmt rffd d n fd d ndd dd} dd} | | | |dur } | dddnt j jjstd         d& fdd  f dd|jdd jdD]} | qΈ D]} | qz|j} Wn tyYnw| r| dd t }d!|d"|td#d$|D]`\}}zt|Wnt y;td%||fdwt|trRt t |d'it|q t|dt!set t ||q t|dt!rt t ||dit|dq |r "dSdS)(a Plot the given tree using matplotlib (or pylab). The graphic is a rooted tree, drawn with roughly the same algorithm as draw_ascii. Additional keyword arguments passed into this function are used as pyplot options. The input format should be in the form of: pyplot_option_name=(tuple), pyplot_option_name=(tuple, dict), or pyplot_option_name=(dict). Example using the pyplot options 'axhspan' and 'axvline':: from Bio import Phylo, AlignIO from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor constructor = DistanceTreeConstructor() aln = AlignIO.read(open('TreeConstruction/msa.phy'), 'phylip') calculator = DistanceCalculator('identity') dm = calculator.get_distance(aln) tree = constructor.upgma(dm) Phylo.draw(tree, axhspan=((0.25, 7.75), {'facecolor':'0.5'}), ... axvline={'x':0, 'ymin':0, 'ymax':1}) Visual aspects of the plot can also be modified using pyplot's own functions and objects (via pylab or matplotlib). In particular, the pyplot.rcParams object can be used to scale the font size (rcParams["font.size"]) and line width (rcParams["lines.linewidth"]). :Parameters: label_func : callable A function to extract a label from a node. By default this is str(), but you can use a different function to select another string associated with each node. If this function returns None for a node, no label will be shown for that node. do_show : bool Whether to show() the plot automatically. show_confidence : bool Whether to display confidence values, if present on the tree. axes : matplotlib/pylab axes If a valid matplotlib.axes.Axes instance, the phylogram is plotted in that Axes. By default (None), a new figure is created. branch_labels : dict or callable A mapping of each clade to the label that will be shown along the branch leading to it. By default this is the confidence value(s) of the clade, taken from the ``confidence`` attribute, and can be easily toggled off with this function's ``show_confidence`` option. But if you would like to alter the formatting of confidence values, or label the branches with something other than confidence, then use this option. label_colors : dict or callable A function or a dictionary specifying the color of the tip label. If the tip label can't be found in the dict or label_colors is None, the label will be shown in black. rNz4Install matplotlib or pylab if you want to use draw.cSs t||kr tt|St|Sr)rMrH)confrrrconf2strms  zdraw..conf2strcsNz|j}Wn tyYn wdfdd|DS|jdur%|jSdS)N/c3s|]}|jVqdSr)value)r$cnfrrrr&|sz4draw..format_branch_label..) confidencesAttributeErrorr~ confidence)rrrrrformat_branch_labelus    z!draw..format_branch_labelcSsdSrrrrrrrscs |Srgetr) branch_labelsrrrs z.get_label_colorcs |dSNblackrrrrrrs cSsdSrrrrrrrscSs$|}t|s|jdd}|S)zeCreate a mapping of each clade to its horizontal position. Dict of {clade: x-coord} TrK)rQrRrS)rrQrrrget_x_positionss  zdraw..get_x_positionscsJ|fddtt|Dfdd|jjr#|jS)zCreate a mapping of each clade to its vertical position. Dict of {clade: y-coord}. Coordinates are negative, and integers for tips. csi|] \}}||qSrr)r$r3tip) maxheightrrr<sz1draw..get_y_positions..csB|D] }|vr |q|jd|jdd|<dS)Nrr]g@r^r`)rcheightsrrrcs z/draw..get_y_positions..calc_row)count_terminalsr)reversedr}rr_rer)rcrrrget_y_positionss  zdraw..get_y_positionsr"zInvalid argument for axes: F horizontalr.1c s|s|dkrj|||||ddS|r,|dkr,j||f||fgg||ddS|s=|dkr=j||||ddS|rW|dkrYj||f||fgg||ddSdSdS)zCreate a line with or without a line collection object. Graphical formatting of the lines representing clades in the plot can be customized by altering this function. r)rlwvertical)rN)hlinesr*LineCollectionvlines) use_linecollection orientationy_herex_startx_herey_boty_toprr)axeshorizontal_linecollections mpcollectionsvertical_linecollectionsrrdraw_clade_liness"    zdraw..draw_clade_linesc s|}|}t|dr|jdur|j}t|dr)|jdur)|jjd}dd|||||d|}|d|jjfvrOj||d|d |d |}|rcjd ||||d d d |jr|jd}|jd} dd|| |||d|D] } | |||qdSdS)z3Recursively draw a tree, down from the given clade.rNrlines.linewidthTr)rrrrrrrrgcenter)verticalalignmentrg?small)fontsizehorizontalalignmentrr]r)rrrrrrr) r rr rrcParams __class____name__textr_) rrrrrrr conf_labelrrr4) rrwrrr label_funcpltx_posnsy_posnsrrrwsb    zdraw..draw_cladekrz branch lengthrZgg?g?g?zKeyword argument "%s=%s" is not in the format pyplot_option_name=(tuple), pyplot_option_name=(tuple, dict), or pyplot_option_name=(dict) ) Frrrrrrrrr)#matplotlib.pyplotpyplotrpylabrmatplotlib.collections collections isinstancedictcallable TypeErrorfigure add_subplot matplotlibrAxes ValueErrorrradd_collectionnamer set_title set_xlabel set_ylabelrRrSset_xlimset_ylimrWlistr(rHtupleshow)rrdo_showshow_confidencerrrargskwargsrrfigr3rxmaxkeyrr)rrrrwrrrrrrrrrrrrdrawsB       !9           $ r)Nr!)NrG) __doc__rTr{Biorr rFrrHrrrrrs  B fa