DUfeddlmZddlmZddlmZddlZddlZ ddl m Z ddl m Z mZmZmZddlmZmZddlZddlZd Zd d Zd Z d!dZ d!dZ d"dZd#dZ d$dZ d%dZ d&dZdZ dS)') combinations)partial)toeplitzN)numutils)is_compatible_viewframeis_valid_expectedis_cooler_balancedis_track)view_from_trackalign_track_with_coolerci||SN)abs Q/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/api/saddle.py _merge_dictrs a:1:leftctj|}tjtj|||dz }tjdt |z dt |}||S)zmask_bad_bins Return array `x`'s empirical CDF value(s) at the points in `v`. This is based on the :func:`statsmodels.distributions.ECDF` step function. This is the inverse of `quantile`. )side?)npasarray searchsortedsortlinspacelen)xvrindys r_ecdfr%s` 1 A /"'!**ad 3 3 3a 7C C#a&&L#s1vv..A S6Mrc ~tj|}tj|dz}tj||fi|S)zz Return the values of the quantile cut points specified by fractions `q` of a sequence of data given by `x`. d)rr nanpercentile)r!qkwargsps r _quantiler,$s> 1 A 1 A Aq + +F + ++rweight balanced.avgnamecdddg|D|fd}|S)a Construct a function that returns intra-chromosomal OBS/EXP for symmetrical regions defined in view_df. Used in `get_saddle()`. Parameters ---------- clr : cooler.Cooler Observed matrix. expected : DataFrame Diagonal summary statistics for a number of regions. view_df: viewframe Viewframe with genomic regions. clr_weight_name : str Name of the column in the clr.bins to use as balancing weights. expected_value_col : str Name of the column in expected used for normalizing. view_name_col : str Name of column in view_df with region names. Returns ------- getexpected(reg, _). 2nd arg is ignored. c$i|] \}}||jSrvalues.0kr!s r z,_make_cis_obsexp_fetcher..Qs0 Aq 18rregion1region2ct j|}t j|}||}t ||fd|jd}||z S)Nbalancer)tuplelocmatrixfetchrshape) reg1reg2 reg1_coords reg2_coordsobs_matexp_matclrclr_weight_nameexpectedview_dfs r _fetch_cis_oez/_make_cis_obsexp_fetcher.._fetch_cis_oeWsGK-.. GK-.. **_*55;;KUU8D$J/0B'-2B0BCDD  r)groupby set_index)rHrJrKrIexpected_value_col view_name_colrLs```` r_make_cis_obsexp_fetcherrQ/sD$$i%;<<=OPH ..G!!!!!!!! rcF|tjr fd}|Sttjjjur6dddg|Dfdfd}|Std)a Construct a function that returns OBS/EXP for any pair of chromosomes. Used in `get_saddle()`. Parameters ---------- clr : cooler.Cooler Observed matrix. expected : DataFrame or scalar Average trans values. If a scalar, it is assumed to be a global trans expected value. If a tuple of (dataframe, name), the dataframe must have a MultiIndex with 'region1' and 'region2' and must also have a column labeled ``name``, with the values of expected. view_df: viewframe Viewframe with genomic regions. clr_weight_name : str Name of the column in the clr.bins to use as balancing weights expected_value_col : str Name of the column in expected used for normalizing. view_name_col : str Name of column in view_df with region names. Returns ----- getexpected(reg1, reg2) ctj|}tj|}||}|z SNr;r=r>r?r@) rBrCrDrErFrHrIrJrKs r_fetch_trans_oez3_make_trans_obsexp_fetcher.._fetch_trans_oes` D 122K D 122Kjjj99??[GX% %rc$i|] \}}||jSrr2r4s rr7z._make_trans_obsexp_fetcher..s0   1 qx   rr8r9c||fvr ||fS||fvr ||fStd||)Nz8trans-exp index is missing a pair of chromosomes: {}, {})keysKeyErrorformat)r8r9rJs r_fetch_trans_expz4_make_trans_obsexp_fetcher.._fetch_trans_exps{!X]]__44 0117#x}}66 011#VGW55rct j|}t j|}||}||}||z SrTrU) rBrCrDrErFexpr\rHrIrKs rrVz3_make_trans_obsexp_fetcher.._fetch_trans_oesq D 122K D 122Kjjj99??[G#"4..CS= rzUnknown type of expected) rNrisscalartypepdcoreframe DataFramerM ValueError)rHrJrKrIrOrPrVr\s```` @r_make_trans_obsexp_fetcherrfasL ..G {8-5 & & & & & & & & h27=2 2 2   (()Y)?@@AST         ! ! ! ! ! ! ! !3444rFc ||jd} |||} ||krtj| dz|D]"} tj| tj| #|dkrytjtj| jd | tj|dz| jdD]"} tj| tj| #|r#td||t| D]} ||| k} t| D]}|||k}| | ddfdd|f}|tj |}|| |fxxtj |z cc<|| |fxxtt|z cc<dS)z Helper function to aggregate across region pairs. If regions are identical, also masks returned matrices below min_diag and above max_diag. Used in `get_saddle()`. rrzregions {} vs {}N)rArarangerset_diagnanappendprintr[rangeisfinitesumfloatr )SC getmatrix digitizedrBrCmin_diagmax_diagverbosen_binsr?dirow_maskjcol_maskdatas r _accumulatersWQZF YtT " "F t||H9q=(33 1 1A  fbfa 0 0 0 0 q==Y 6<?*XI66 (Q, Q88 5 5!&"&!44445  ''d33444 6]]((T?a'v ( (A !+H(AAA+&qqq({3D D))*D adGGGrvd|| #GGG adGGGuSYY'' 'GGGG  (((rc||td|8|\}}||krtdtj|||dz}|||fS|c|\}}|dks|dkrtd||krtdtj|||dz} t|| }|||fStd ) z Helper function to make bins for `get_digitized()`. Nakes binedges in real space from value limits provided by vrange, or in quantile space from quantile limits provided by qrange. Nz,only one of vrange or qrange can be suppliedz+vrange does not satisfy vrange[0] values assigned to bins defined by vrange or qrange - `0` <-> left outlier values - `n+1` <-> right outlier values - `-1` <-> missing data (NaNs) z!n_bins must be provided as an intT raise_errorsrgrrF)rightrhr) categoriesorderedN)r`intrer copycolumnsastyperfloat64r3rdigitizer>maxisnullraCategoricalDtyperjlist)trackrzrrdigitized_suffixrvtrack_value_col digitized_colrrrrmaskdigitized_catss rrrsd F||3<=== U&&&& ImA&O#&66M)..00L&&'DEELL%fVFHb" "{<OOOIm M/"bfX&6&66G  ! ( ( * *D)+IM$ %&(9R!,,dN  -!@AAI$u}RaR011]OCDI h rc  t|turKt|||d|}t|jddddf|||d\}}|jd}n||}|jd}t ||did t|jdtj jjj urtd ||j jj}t!||d kd z }ntd t#|n7 t%|dd}n"#t&$r}td|d}~wwxYw t)|||| gd}n"#t&$r}td|d}~wwxYw|r: t+||d }n&#t&$r}td|d|d}~wwxYwi}D]+\}}t/j||}|||| <,|dkr?t3t5  }t7|| | |}n]|dkrHt3t9 d } fd|D}t;|| | |}ntdt=j|d z|d zf}t=j|d z|d zf}|D]\}}tA||||||| | | ||j!z }||j!z }| r|dd dd f}|dd dd f}||fS)a Get a matrix of average interactions between genomic bin pairs as a function of a specified genomic track. The provided genomic track is either: (a) digitized inside this function by passing 'n_bins', and one of 'v_range' or 'q_range' (b) passed as a pre-digitized track with a categorical value column as generated by `get_digitized()`. Parameters ---------- clr : cooler.Cooler Observed matrix. expected : DataFrame in expected format Diagonal summary statistics for each chromosome, and name of the column with the values of expected to use. contact_type : str If 'cis' then only cis interactions are used to build the matrix. If 'trans', only trans interactions are used. track : DataFrame A track, i.e. BedGraph-like dataframe, which is digitized with the options n_bins, vrange and qrange. Can optionally be passed as a pre-digitized dataFrame with a categorical value column, as generated by get_digitzied(), also passing n_bins as None. n_bins : int or None number of bins for signal quantization. If None, then track must be passed as a pre-digitized track. vrange : tuple Low and high values used for binning track values. See get_digitized(). qrange : tuple Low and high values for quantile binning track values. Low must be 0.0 or more, high must be 1.0 or less. Only one of vrange or qrange can be passed. See get_digitzed(). view_df: viewframe Viewframe with genomic regions. If none, generate from track chromosomes. clr_weight_name : str Name of the column in the clr.bins to use as balancing weights. Using raw unbalanced data is not supported for saddles. expected_value_col : str Name of the column in expected used for normalizing. view_name_col : str Name of column in view_df with region names. min_diag : int Smallest diagonal to include in computation. Ignored with contact_type=trans. max_diag : int Biggest diagonal to include in computation. Ignored with contact_type=trans. trim_outliers : bool, optional Remove first and last row and column from the output matrix. verbose : bool, optional If True then reports progress. drop_track_na : bool, optional If True then drops NaNs in input track (as if they were missing), If False then counts NaNs as present in dataframe. In general, this only adds check form chromosomes that have all missing values, but does not affect the results. Returns ------- interaction_sum : 2D array The matrix of summed interaction probability between two genomic bins given their values of the provided genomic track. interaction_count : 2D array The matrix of the number of genomic bin pairs that contributed to the corresponding pixel of ``interaction_sum``. T)rKrImask_clr_bad_bins drop_track_naNr)rrrrgrrrzwhen n_bins=None, saddle assumes the track has been pre-digitized and the value column is a pandas categorical. See get_digitized().rhrz&n_bins must be provided as int or None) check_sortingrz0view_df is not a valid viewframe or incompatible) verify_coolerexpected_value_colsrz#provided expected is not compatiblez#provided cooler is not balanced or z is missingcis)rPrOrItranscg|]V}dj|dkjdj|dkjkT|WS)chromrr)r>r3)r5r|rKrPs r zsaddle..sz    $W]%;qt%CDK7#' (>!A$(FGNOO OOOrz5Allowed values for contact_type are 'cis' or 'trans'.)rwrxryr)"r`rr rilocrr rdtypesrarbrredtyperr3r r r Exceptionr r iterrowsbioframeselectrziprQrrfrzerosrT) rHrJr contact_typerzrrrKrIrOrPrwrx trim_outliersryrdigitized_trackrrcats_edigitized_tracksnumreg digitized_regsupportsruinteraction_suminteraction_countrBrCs ` ` rsaddlerQsh F||s'  +"'    %- Jqqq"1"u  ! % % % !(/2 '/2 }g677dKKKK '* + +7>(9 : :=  }-3>ET$)_%%)ABBB!/22 X'"! AA  X X XOPPVW W X G    "!  GGG>??QFG "3dKKKAA   RoRRR   $$&&LLS == /<]/K]+,,uGM2GM4JKKLL,   '1+       W]%;Q??@@        /   '1+    PQQQh FQJ788O&1*fqj!9::   d       ((O*,,:)!B$"*5-adAbDj9 - --sH5E E(E##E(,F F" FF"(F;; GGGrrcoolwarmlog?cJtjdtddlm}m}ddlm}m}ddl m }ddl m }Gfdd|j }|jd }||j}t!|||| \}}||jd jt$}||d k|t)|d zkz}t+j|t)|d z } ||\}!}"||\}!}"t+j|!|"|d z}|jd}#t+j||\}$}%|}&|#|z dkr|&d d d d f}&| d d } |t5||}i}'|d d gdgddd}(|1t7d})t9|)||ni}|jd5i|}|dkr|}*n#|dkr|}*nt=d||(dx|'d<}+t7|d},t9|,||ni}|+j |$|%|&fd|*i|}-|!j"#dt7d| d }.t9|.||ni}||(d |'d!|'d"<|j$|dd ft+j%|| d#d$||&|&d |&d|'|"|!|!j(d%#d|!j(d&#d|!j(d'#d|!j)#d||(d |'d(|'d)<|j*|dd ft+j%|| d#d*||&|!|"|!j(d%#d|!j(d+#d|!j(d'#d|!j)#d|!j"#d||(d,|'d-<t7d.| pd/0}/t9|/||ni}|dkr_][|j+|-fi|x|'d1<}0d2}1d,}2t+j,t+j|2|1z|1z }3|0-|3nD|j+|-fd3|i|x|'d1<}0|0j.j"/||'d0|!|"|'d1|"|!|2d|3d4| |'d)4| | |'d5| | |'d"6| |'S)6a Generate a saddle plot. Parameters ---------- track : pd.DataFrame See get_digitized() for details. saddledata : 2D array-like Saddle matrix produced by `make_saddle`. It will include 2 flanking rows/columns for outlier signal values, thus the shape should be `(n+2, n+2)`. cmap : str or matplotlib colormap Colormap to use for plotting the saddle heatmap scale : str Color scaling to use for plotting the saddle heatmap: log or linear vmin, vmax : float Value limits for coloring the saddle heatmap color : matplotlib color value Face color for margin bar plots fig : matplotlib Figure, optional Specified figure to plot on. A new figure is created if none is provided. fig_kws : dict, optional Passed on to `plt.Figure()` heatmap_kws : dict, optional Passed on to `ax.imshow()` margin_kws : dict, optional Passed on to `ax.bar()` and `ax.barh()` cbar_kws : dict, optional Passed on to `plt.colorbar()` subplot_spec : GridSpec object Specify a subregion of a figure to using a GridSpec. Returns ------- Dictionary of axes objects. zGenerating a saddleplot will be deprecated in future versions, please see https://github.com/open2c_examples for examples on how to plot saddles.r)GridSpecGridSpecFromSubplotSpec) NormalizeLogNorm)tickerNc,eZdZdfd Zdfd ZdS)&saddleplot..MinOneMaxFormatterNcHtdzdzdzdg|_dS)N r)set _sublabels)selflocsvmaxvmins rset_locsz/saddleplot..MinOneMaxFormatter.set_locss)!4"9r>4"9a"@AADOOOrcB|dfvrdSd|S)Nrz{x:g})r!)r[)rr!posrrs r__call__z/saddleplot..MinOneMaxFormatter.__call__s-q$''r~~~***rr)__name__ __module__ __qualname__rr)rrsrMinOneMaxFormatterrsb B B B B B B B + + + + + + + + +rrrgrrhr) minlengthr) subplot_spec)g?rg?g?)nrowsncols width_ratios height_ratioswspacehspace)r)figsizer)rrlinearz.Only linear and log color scaling is supportedr ax_heatmapT)cmap rasterizednormFr6) edgecolor facecolor linewidth)sharey ax_margin_yedge)heightwidthaligntopbottomr)sharex ax_margin_x)rrrrrax_cbarg?r)fractionlabelcbarrr[offr)7warningswarnDeprecationWarningmatplotlib.gridspecrrmatplotlib.colorsrr matplotlibrmatplotlib.pyplotpyplot LogFormatterrr3rrrrr rbincountrrAmeshgridrdictrfigureresubplot pcolormeshgcayaxis set_visiblebarhdiffxlimylimspinesxaxisbarcolorbartrunc set_ticksaxset_minor_formatterset_xlimset_ylimgridaxis set_title set_xlabel set_ylabel)4r saddledatarzrrrscalerrcolortitlexlabelylabelclabelfigfig_kws heatmap_kws margin_kwscbar_kwsrrrrrrpltrrrrrr!histrrnXYrtr(gsfig_kws_defaultrr$heatmap_kws_defaultimgmargin_kws_defaultcbar_kws_defaultcbdecimal nsegmentscd_tickss4 `` r saddleplotrH7sz M _ FEEEEEEE44444444!!!!!!######++++++++V0+++mA&O)0L!)vf U U UOX/23:AA#FFKKMMA 1r6a#h--!++ ,-A ;qCMMA$5 6 6 6D B B;r2vz22 A ;x * *DAqA F q adAbDjMAbDz2NNN D "]]#mm    B {v...o':MwwSUVVcj##7## ~~wDt,,, (  yd...IJJJ!kk"Q%000DDT:::K,C[[K "-1a : :d :k : :CGGIIO&&&uJJJ**@JJbJ++beD4F+GGD CH"  gh//t6MWHHSXXZZ]CHHJJqM***HHRGGIIU''...GGIIX**5111GGIIV((///GGIIO&&&++beD4F+GGD CG" WX..t6MWHHRGGIIU''...GGIIW))%000GGIIV((///GGIIO&&&GGIIO&&&kk"Q%((DOS "===+9MXXSUVVH T-$2B(CL99999V r 8BKdI>>HIIGS X(CLVV5G5G5I5IVXVVVV r  ''(:(:(<(<=== B'''B'''HHUOOOHHUOOO  ]%%e,,,  \%%f---  ]&&v... Krc|j\}}||krtdtj|}t d|D]1}tj|d|d|ftj|||z |||z |fz}tj|d|d|ftj|||z |||z |fz}||z }tj|d|||z |ftj|||z |d|fz} tj|d|||z |ftj|||z |d|fz} | | z } || z ||<3|S)a: Parameters ---------- S, C : 2D arrays, square, same shape Saddle sums and counts, respectively Returns ------- 1D array Ratios of cumulative corner interaction scores, where the saddle data is grouped over the AA+BB corners and AB+BA corners with increasing extent. z`saddledata` should be square.rr)rArerrronansum) rsrtmr;ratiosr6 intra_sum intra_countintra inter_sum inter_countinters rsaddle_strengthrSs 7DAqAvv9::: Xa[[F 1a[[ " "Ia!QqSk**RYqQAEAI9M7N-O-OO i!A#qs( ,,ry1q519a!eai;O9P/Q/QQ K'Ia!QUQY/0029Qq1uqy!A#~=N3O3OO i!A#q1uqy. 122RYqQAaC?P5Q5QQ K'EMq Mr)r)r-r.r/)rgrhF)NN)NNr) NNNr-r.r/rgrhFFF)NrrrrrNNNNNNNNNNN)! itertoolsr functoolsr scipy.linalgrnumpyrpandasralibr lib.checksrr r r lib.commonr r rrrr%r,rQrfrrrrrHrSrrrr\s@""""""!!!!!! BAAAAAAA    ,,,% ////l% U5U5U5U5rNS!(!(!(!(HEEEEH   PPPPr   %   !c.c.c.c.T           )FFFFRr