ó jÜxec@ sddlmZddlZddlZddlZejddkrcddlZej dƒnddl j Z ddl mZddlmZddlmZdd lmZdd lmZmZdd lmZmZdd lmZd dd„ƒYZdS(iÿÿÿÿ(tdivisionNiitTkAgg(t Rectangle(tAxes(tGlyph(tvalidate_matrix(tcheckt handle_errors(tget_color_dicttget_rgb(ttransform_matrixtLogocB sOeZdZed!ddededdedddd!d!dd"d „ƒZd „Zed!d „ƒZ eddd „ƒZ ed!d!ddd!d „ƒZ ed„ƒZ ed„ƒZ ed„ƒZeddd!d!d!dd„ƒZedddd„ƒZeddddd„ƒZed#eddd!d„ƒZed„Zd „ZRS($ss Logo represents a basic logo, drawn on a specified axes object using a specified matrix, which is supplied as a pandas dataframe. attributes ---------- df: (pd.DataFrame) A matrix specifying character heights and positions. Rows correspond to positions while columns correspond to characters. Column names must be single characters and row indices must be integers. color_scheme: (str, dict, or array with length 3) Specification of logo colors. Default is 'gray'. Can take a variety of forms. - (str) A built-in Logomaker color scheme in which the color of each character is determined that character's identity. Options are, + For DNA/RNA: 'classic', 'grays', or 'base_paring'. + For protein: 'hydrophobicity', 'chemistry', or 'charge'. - (str) A built-in matplotlib color name such as 'k' or 'tomato' - (list) An RGB array, i.e., 3 floats with values in the interval [0,1] - (dict) A dictionary that maps characters to colors, E.g., {'A': 'blue', 'C': 'yellow', 'G': 'green', 'T': 'red'} font_name: (str) The character font to use when rendering the logo. For a list of valid font names, run logomaker.list_font_names(). stack_order: (str) Must be 'big_on_top', 'small_on_top', or 'fixed'. If 'big_on_top', stack characters away from x-axis in order of increasing absolute value. If 'small_on_top', stack glyphs away from x-axis in order of decreasing absolute value. If 'fixed', stack glyphs from top to bottom in the order that characters appear in the data frame. center_values: (bool) If True, the stack of characters at each position will be centered around zero. This is accomplished by subtracting the mean value in each row of the matrix from each element in that row. baseline_width: (float >= 0.0) Width of the logo baseline, drawn at value 0.0 on the y-axis. flip_below: (bool) If True, characters below the x-axis (which correspond to negative values in the matrix) will be flipped upside down. shade_below: (float in [0,1]) The amount of shading to use for characters drawn below the x-axis. Larger numbers correspond to more shading (i.e., darker characters). fade_below: (float in [0,1]) The amount of fading to use for characters drawn below the x-axis. Larger numbers correspond to more fading (i.e., more transparent characters). fade_probabilities: (bool) If True, the characters in each stack will be assigned an alpha value equal to their height. This option only makes sense if df is a probability matrix. For additional customization, use Logo.fade_glyphs_in_probability_logo(). vpad: (float in [0,1]) The whitespace to leave above and below each character within that character's bounding box. Note that, if vpad > 0, the height of the character's bounding box (and not of the character itself) will correspond to values in df. vsep: (float >= 0) Amount of whitespace to leave between the bounding boxes of rendered characters. Unlike vpad, vsep is NOT relative to character height. alpha: (float in [0,1]) Opacity to use when rendering characters. Note that, if this is used together with fade_below or fade_probabilities, alpha will multiply existing opacity values. show_spines: (None or bool) Whether a box should be drawn around the logo. For additional customization of spines, use Logo.style_spines(). ax: (matplotlib Axes object) The matplotlb Axes object on which the logo is drawn. zorder: (int >=0) This governs what other objects drawn on ax will appear in front or behind the rendered logo. figsize: ([float, float]): The default figure size for the rendered logo; only used if ax is not supplied by the user. **kwargs: Additional key word arguments to send to the Glyph constructor. tsanst big_on_topgà?ggð?ii g@cK s||_||_||_||_||_||_||_||_| |_| |_ | |_ | |_ | |_ ||_ ||_||_||_||_t|_|jƒt|jƒ|_tjg|jjD] }|^qÚƒ|_t|jƒ|_t|j|jƒ|_tjg|jjD] }|^q/ƒ|_|jrkt |jdt!ƒ|_n|jdkr§t#j$ddd|jƒ\}}||_n|j%|_&|j'ƒ|j(d|jd|jd|jƒ|j r|j)ddd dƒn|j*ƒdS( Nt center_valuesitfigsizetshadetfadetfliptv_alpha0itv_alpha1(+tdft color_schemet font_namet stack_orderRtbaseline_widtht flip_belowt shade_belowt fade_belowtfade_probabilitiestvpadtvseptalphat show_spinestzorderRtaxt glyph_kwargstFalsethas_been_drawnt _input_checkstlentLtnptarraytcolumnstcstCRtrgb_dicttindextpsR tTruetNonetplttsubplotstfiguretfigt_compute_glyphststyle_glyphs_belowtfade_glyphs_in_probability_logotdraw(tselfRRRRRRRRRRRRR R!R#R"RtkwargstctpR7((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyt__init__|sN                    ++ !       cC sôt|jƒ|_tt|jtƒdt|jƒƒdddh}t|j|kd|j|fƒtt|jt ƒdt|jƒƒtt|j t t fƒdt|j ƒƒt|j dkd |j ƒtt|j t ƒd t|j ƒƒtt|jt t fƒd t|jƒƒtd|jkoHd knd ƒtt|jt t fƒdt|jƒƒtd|jkošd kndƒtt|jt ƒdt|jƒƒtt|jt t fƒdt|jƒƒtd|jkod kndƒtt|jt t fƒdt|jƒƒt|jdkd|jƒtt|jt t fƒdt|jƒƒtd|jko­d kndƒtt|jt ƒp×|jdkdt|jƒƒtt|jtƒp |jdkdt|jƒƒtt|jt t fƒdt|jƒƒtt|jtttjfƒdt|jƒƒt|jƒ|_tt|jƒdkdƒtt g|jD]'}t|t t fƒoà|dk^q¼ƒdƒdS( s Validate parameters passed to the Logo constructor EXCEPT for color_scheme; that is validated in the Logo constructor s(type(font_name) = %s must be of type strR t small_on_toptfixeds stack_order = %s; must be in %s.s/type(center_values) = %s; must be of type bool.s0type(baseline_width) = %s must be of type numbergs"baseline_width = %s must be >= 0.0s,type(flip_below) = %s; must be of type bool s,type(shade_below) = %s must be of type floatgð?s#shade_below must be between 0 and 1s+type(fade_below) = %s must be of type floats"fade_below must be between 0 and 1s4type(fade_probabilities) = %s; must be of type bool s%type(vpad) = %s must be of type floatsvpad must be between 0 and 1s.type(vsep) = %s; must be of type float or int is!vsep = %d must be greater than 0 s&type(alpha) = %s must be of type floatsalpha must be between 0 and 1s6show_spines = %s; show_spines must be None or boolean.s5ax = %s; ax must be None or a matplotlib.Axes object.s+type(zorder) = %s; zorder must be a number.s/type(figsize) = %s; figsize must be array-like.isfigsize must have length two.s2all elements of figsize array must be numbers > 0.N(!RRRt isinstanceRtstrttypeRRtboolRtinttfloatRRRRRRR R!R3treprR#RR"RttupletlistR*tndarrayR(tall(R<tvalid_stack_orderstn((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyR'Ùsv&&!! 4cK s¸|dk r0||_t|j|jƒ|_nx=dddgD],}||jƒkr@|||j|tset_attributes(R<RR=tkeytg((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyt style_glyphsLs$   cC sstt|ttfƒdt|ƒƒtd|ko@dknd|ƒtt|ttfƒdt|ƒƒtd|kodknd|ƒt||kd||fƒt|jdd ƒ|_x|jD]’}x‰|jD]~}|jj ||f}|j j ||f}||kr0d }n'||krEd }n||||}|j d |ƒqéWqÙWd S(sv Fades glyphs in probability logo according to value. parameters ---------- v_alpha0, v_alpha1: (number in [0,1]) Matrix values marking values that are rendered using alpha=0 and alpha=1, respectively. These values must satisfy v_alpha0 < v_alpha1. returns ------- None s$type(v_alpha0) = %s must be a numberggð?s.v_alpha0 must be between 0 and 1; value is %f.s$type(v_alpha1) = %s must be a numbers-v_alpha1 must be between 0 and 1; value is %fsCmust have v_alpha0 < v_alpha1;here, v_alpha0 = %f and v_alpha1 = %ft matrix_typet probabilityiiR N( RRCRHRGRERRR1R-tloctglyph_dfRT(R<RRR?R>tvRVR ((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyR:ƒs0       c K s#|dk rt|ƒ}n|dk r‚tt|ttfƒdt|ƒƒt|ƒ|_td|kovdkndƒntt|ttfƒdt|ƒƒtd|koÂdknd|ƒtt|ttfƒdt|ƒƒtd|kodknd |ƒ|dk rKtt|tƒd t|ƒƒnxÑ|j D]Æ}x½|j D]²}|j j ||f} | dkre|j j ||f} |dkrÁt| jƒ} n|} |dkrß| j} n|} | jd | d|d | d|d ||qeqeWqUWdS(s Modifies the properties of all characters drawn below the x-axis. parameters ---------- color: (color specification) Color to use before shade is applied. alpha: (number in [0,1]) Opacity to use when rendering characters, before fade is applied. shade: (number in [0,1]) The amount to shade characters below the x-axis. fade: (number in [0,1]) The amount to fade characters below the x-axis. flip: (bool) If True, characters below the x-axis will be flipped upside down. **kwargs: Keyword arguments to pass to Glyph.set_attributes(), but only for characters below the x-axis. returns ------- None s'type(alpha) = %s must be a float or intigð?s-alpha must be between 0.0 and 1.0 (inclusive)s!type(shade) = %s must be a numbergs+shade must be between 0 and 1; value is %f.s type(fade) = %s must be a numbers)fade must be between 0 and 1; value is %fs&type(flip) = %s; must be of type bool RPR RN(R3R RRCRHRGRER RFR1R-RRZR[RPRT( R<RPR RRRR=R?R>R\RVt this_colort this_alpha((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyR9ÅsL(          cK sÄtt|tƒdt|ƒƒt||jjkd|ƒtt|tƒdt|ƒƒtt|ƒdkdt|ƒƒt||jj kd|ƒ|jj ||f}|j |dS(s Modifies the properties of a single character in Logo. parameters ---------- p: (int) Position of modified glyph. Must index a row in the matrix df passed to the Logo constructor. c: (str of length 1) Character to modify. Must be the name of a column in the matrix df passed to the Logo constructor. **kwargs: Keyword arguments to pass to Glyph.set_attributes() returns ------- None s type(p) = %s must be of type intsp=%s is not a valid positions type(c) = %s must be of type strisc = %s; must have length 1.sc=%s is not a valid characterN( RRCRGRER[R0RDR(RIR,RZRT(R<R?R>R=RV((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pytstyle_single_glyph1s  cK s§tt|tƒdt|ƒƒtt|ƒ|jkdt|ƒd|jƒxOt|jjƒD];\}}||}||j krd|j |||qdqdWdS(sÐ Restyles the glyphs in a specific sequence. parameters ---------- sequence: (str) A string the same length as the logo, specifying which character to restyle at each position. Characters in sequence that are not in the columns of the Logo's df are ignored. **kwargs: Keyword arguments to pass to Glyph.set_attributes() returns ------- None s'type(sequence) = %s must be of type strs sequence to restyle (length %d) s*must have same length as logo (length %d).N( RRCRDRER(R)t enumerateR[R0R-R_(R<tsequenceR=tiR?R>((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pytstyle_glyphs_in_sequencecs  cK s=tt|tƒdt|ƒƒ|jd|d||dS(s1 Draws a rectangular box highlighting a specific position. parameters ---------- p: (int) Single position to highlight. **kwargs: Other parameters to pass to highlight_position_range() returns ------- None s type(p) = %s must be of type inttpmintpmaxN(RRCRGREthighlight_position_range(R<R?R=((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pythighlight_positionstyellowiþÿÿÿc K s|jjƒ\} } tt|ttfƒdt|ƒƒtt|ttfƒdt|ƒƒt||kdƒtt|ttfƒo•|dkdt|ƒƒ|dk rÁt |ƒ}n|dk rÜt |ƒ}n|dkrñ| }n&tt|ttfƒdt|ƒƒ|dkr,| }n&tt|ttfƒdt|ƒƒt||kd||fƒtt|ttfƒd t|ƒƒ|d |} |} ||d d |}||}t d | | fd|d|d|d|d|| }|jj |ƒdS(s Draws a rectangular box highlighting multiple positions within the Logo parameters ---------- pmin: (int) Lowest position to highlight. pmax: (int) Highest position to highlight. padding: (number >= -0.5) Amount of padding to add on the left and right sides of highlight. color: (None or matplotlib color) Color to use for highlight. Can be a named matplotlib color or an RGB array. edgecolor: (None or matplotlib color) Color to use for highlight box edges. Can be a named matplotlib color or an RGB array. floor: (None number) Lowest y-axis extent of highlight box. If None, is set to ymin of the Axes object. ceiling: (None or number) Highest y-axis extent of highlight box. If None, is set to ymax of the Axes object. zorder: (number) This governs which other objects drawn on ax will appear in front or behind of the highlight. Logo characters are, by default, drawn in front of the highlight box. returns ------- None s type(pmin) = %s must be a numbers type(pmax) = %s must be a numberspmin <= pmax not satisfied.gà¿s%padding = %s must be a number >= -0.5s!type(floor) = %s must be a numbers#type(ceiling) = %s must be a numbers;must have floor <= ceiling; as is, floor = %f, ceiling = %ss'type(zorder) = %s; must a float or int.gà?iitxytwidththeightt facecolort edgecolorR"N( R#tget_ylimRRCRHRGRERIR3R Rt add_patch(R<RdRetpaddingRPRmtfloortceilingR"R=tymintymaxtxtyRjRktpatch((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyRf«sL4 !         iÿÿÿÿtblackcK s‘tt|ttfƒdt|ƒƒt|ƒ}tt|ttfƒdt|ƒƒt|dkdƒ|jjd|d|d||dS( s‘ Draws a horizontal line along the x-axis. parameters ---------- zorder: (number) This governs what other objects drawn on ax will appear in front or behind the baseline. Logo characters are, by default, drawn in front of the baseline. color: (matplotlib color) Color to use for the baseline. Can be a named matplotlib color or an RGB array. linewidth: (number >= 0) Width of the baseline. **kwargs: Additional keyword arguments to be passed to ax.axhline() returns ------- None s'type(zorder) = %s; must a float or int.s'type(linewidth) = %s; must be a number islinewidth must be >= 0R"RPt linewidthN(RRCRHRGRER R#taxhline(R<R"RPRyR=((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyt draw_baseline"s! is%dc K s(tt|tƒdt|ƒƒtt|tƒo;|dkdt|ƒƒtt|tƒdt|ƒƒtt|ttfƒdt|ƒƒt|jƒ}t |jƒ}t j ||dƒ}||||dk} |j j | ƒg| D]} || ^qõ} |j j| d||dS( s© Formats and styles tick marks along the x-axis. parameters ---------- anchor: (int) Anchors tick marks at a specific number. Even if this number is not within the x-axis limits, it fixes the register for tick marks. spacing: (int > 0) The spacing between adjacent tick marks fmt: (str) String used to format tick labels. rotation: (number) Angle, in degrees, with which to draw tick mark labels. **kwargs: Additional keyword arguments to be passed to ax.set_xticklabels() returns ------- None s%type(anchor) = %s must be of type intisspacing = %s must be an int > 0s"type(fmt) = %s must be of type strs2type(rotation) = %s; must be of type float or int itrotationN(RRCRGRERIRDRHtminR1tmaxR*tarangeR#t set_xtickstset_xticklabels( R<tanchortspacingtfmtR|R=tp_mintp_maxR1txticksR?t xticklabels((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyt style_xticksVs $ttoptbottomtlefttrightc C s*d|_tt|tttfƒdt|ƒƒt|ƒ}ddddh}t||kdt|ƒƒtt|t ƒdt|ƒƒtt|t t fƒdt|ƒƒt|d kd ƒt |ƒ}|dk r¦ttt jf}tt||ƒd t|ƒ|fƒtt|ƒd kd t|ƒd fƒttg|D]}t|t t fƒ^qLƒdt|ƒƒt|d |dkdt|ƒƒnx}|jjjƒD]i\} } | |kr¹| j|ƒ| j|ƒ| j|ƒ|dk r"| j|d |dƒq"q¹q¹WdS(sq Styles the spines of the Axes object in which the logo is drawn. Note: "spines" refers to the edges of the Axes bounding box. parameters ---------- spines: (tuple of str) Specifies which of the four spines to modify. The default value for this parameter lists all four spines. visible: (bool) Whether to show or not show the spines listed in the parameter spines. color: (matplotlib color) Color of the spines. Can be a named matplotlib color or an RGB array. linewidth: (float >= 0) Width of lines used to draw the spines. bounds: (None or [float, float]) If not None, specifies the values between which a spine (or spines) will be drawn. returns ------- None s6type(spines) = %s; must be of type (tuple, list, set) RŠR‹RŒRs/spines has invalid entry; valid entries are: %ss)type(visible) = %s; must be of type bool s'type(linewidth) = %s; must be a number islinewidth must be >= 0s$type(bounds) = %s; must be one of %sislen(bounds) = %d; must be %ds(bounds = %s; all entries must be numbersis,bounds = %s; must have bounds[0] < bounds[1]N(R3R!RRCRJRKtsetRERIRFRHRGR R*RLR(RMR#tspinestitemst set_visiblet set_colort set_linewidtht set_bounds( R<RtvisibleRPRytboundst valid_spinest bounds_typestboundtnametspine((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyt style_spines—sD(     .     cC sftt|tƒdt|ƒƒ|rT|jjƒx|jD]}|jƒq=Wn|jd|j ƒt g|jD]}|j d|j ^qtƒ}t g|jD]}|j d|j ^q¤ƒ}|jj||gƒt g|jD]}|j^qêƒ}t g|jD]}|j^qƒ}|jj||gƒ|jdk rb|jd|jƒndS(s× Draws characters in Logo. parameters ---------- clear: (bool) If True, Axes will be cleared before logo is drawn. returns ------- None s'type(clear) = %s; must be of type bool Rygà?R•N(RRCRFRER#tclearRSR;R{RR}R?RjR~tset_xlimRqRrtset_ylimR!R3Rœ(R<RRVtxmintxmaxRsRt((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyR;ÿs  00%%cC sntjƒ}x|jD]}tj|jj|dd…fƒ}|jdkrbtj|ƒ}n |jdkr¶tj t |ƒƒ}|dk}d||||R-RqR\RrR]RtglyphRV((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyR8,sH % + &(        N(i g@(RŠR‹RŒR(t__name__t __module__t__doc__RR3R%R2R@R'RWR:R9R_RcRgRfR{R‰RœR;R8(((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyR srbK s5?f2*n0<b -((t __future__RtnumpyR*tpandasR¢tsyst version_infot matplotlibtusetmatplotlib.pyplottpyplotR4tmatplotlib.patchesRtmatplotlib.axesRtlogomaker.src.GlyphRtlogomaker.src.validateRtlogomaker.src.error_handlingRRtlogomaker.src.colorsRR tlogomaker.src.matrixR R (((s7/tmp/pip-install-l3LICk/logomaker/logomaker/src/Logo.pyts