matplotlib中的序列標識：aligning xticks

我想用matplotlib繪製sequence logos。整個代碼可以在gist matplotlib中的序列標識：aligning xticks

有關部分是：

class Scale(matplotlib.patheffects.RendererBase): 
    def __init__(self, sx, sy=None): 
     self._sx = sx 
     self._sy = sy 

    def draw_path(self, renderer, gc, tpath, affine, rgbFace): 
     affine = affine.identity().scale(self._sx, self._sy)+affine 
     renderer.draw_path(gc, tpath, affine, rgbFace) 


def draw_logo(all_scores): 
    fig = plt.figure() 
    fig.set_size_inches(len(all_scores),2.5) 
    ax = fig.add_subplot(111) 
    ax.set_xticks(range(len(all_scores))) 

    xshift = 0 
    trans_offset = transforms.offset_copy(ax.transAxes, 
            fig=fig, 
            x=0, 
            y=0, 
            units='points') 


    for scores in all_scores: 
     yshift = 0 
     for base, score in scores: 
      txt = ax.text(0, 
         0, 
         base, 
         transform=trans_offset, 
         fontsize=80, 
         color=COLOR_SCHEME[base], 
         weight='bold', 
         ha='center', 
         family='sans-serif' 
        ) 
     txt.set_clip_on(False) 
     txt.set_path_effects([Scale(1.0, score)]) 
     fig.canvas.draw() 
     window_ext = txt.get_window_extent(txt._renderer) 
     yshift = window_ext.height*score 
     trans_offset = transforms.offset_copy(txt._transform, fig=fig, y=yshift, units='points') 
    xshift += window_ext.width 
    trans_offset = transforms.offset_copy(ax.transAxes, fig=fig, x=xshift, units='points') 


    ax.set_yticks(range(0,3)) 


    seaborn.despine(ax=ax, offset=30, trim=True) 
    ax.set_xticklabels(range(1,len(all_scores)+1), rotation=90) 
    ax.set_yticklabels(np.arange(0,3,1)) 
    plt.show() 


ALL_SCORES1 = [[('C', 0.02247014831444764), 
      ('T', 0.057903843733384308), 
      ('A', 0.10370837683591219), 
      ('G', 0.24803586793255664)], 
     [('T', 0.046608227674354567), 
      ('G', 0.048827667087419063), 
      ('A', 0.084338697696451109), 
      ('C', 0.92994511407402669)], 
     [('G', 0.0), 
      ('T', 0.011098351287382456), 
      ('A', 0.022196702574764911), 
      ('C', 1.8164301607015951)], 
     [('C', 0.020803153636453006), 
      ('T', 0.078011826136698756), 
      ('G', 0.11268374886412044), 
      ('A', 0.65529933954826969)], 
     [('T', 0.017393530660176126), 
      ('A', 0.030438678655308221), 
      ('G', 0.22611589858228964), 
      ('C', 0.45078233627623127)], 
     [('G', 0.022364103549245576), 
      ('A', 0.043412671595594352), 
      ('T', 0.097349627214363091), 
      ('C', 0.1657574733649966)], 
     [('C', 0.03264675899941203), 
      ('T', 0.045203204768416654), 
      ('G', 0.082872542075430544), 
      ('A', 1.0949220710572034)], 
     [('C', 0.0), 
      ('T', 0.0076232429756614498), 
      ('A', 0.011434864463492175), 
      ('G', 1.8867526364762088)], 
     [('C', 0.0018955903000026028), 
      ('T', 0.0094779515000130137), 
      ('A', 0.35637097640048931), 
      ('G', 0.58005063180079641)], 
     [('A', 0.01594690817903021), 
      ('C', 0.017541598996933229), 
      ('T', 0.2774762023151256), 
      ('G', 0.48638069946042134)], 
     [('A', 0.003770051401807444), 
      ('C', 0.0075401028036148881), 
      ('T', 0.011310154205422331), 
      ('G', 1.8624053924928772)], 
     [('C', 0.036479877757360731), 
      ('A', 0.041691288865555121), 
      ('T', 0.072959755514721461), 
      ('G', 1.1517218549109602)], 
     [('G', 0.011831087684038642), 
      ('T', 0.068620308567424126), 
      ('A', 0.10174735408273231), 
      ('C', 1.0009100180696691)], 
     [('C', 0.015871770937774379), 
      ('T', 0.018757547471915176), 
      ('A', 0.32176408355669878), 
      ('G', 0.36505073156881074)], 
     [('A', 0.022798100897300954), 
      ('T', 0.024064662058262118), 
      ('G', 0.24571286522646588), 
      ('C', 0.34070495229855319)]] 

ALL_SCORES2 = [[('A', 0.01653482213365913), 
      ('G', 0.026710097292833978), 
      ('C', 0.035613463057111966), 
      ('T', 0.057235922770358522)], 
     [('C', 0.020055669245080433), 
      ('G', 0.023816107228533015), 
      ('A', 0.031336983195438178), 
      ('T', 0.058913528407423782)], 
     [('T', 0.018666958185377256), 
      ('G', 0.084001311834197651), 
      ('A', 0.093334790926886277), 
      ('C', 0.30333807051238043)], 
     [('C', 0.0), 
      ('G', 0.0), 
      ('A', 0.32027512306044359), 
      ('T', 0.82203948252180525)], 
     [('C', 0.012698627658037786), 
      ('A', 0.053334236163758708), 
      ('T', 0.096509570201087178), 
      ('G', 0.10920819785912497)], 
     [('C', 0.0), 
      ('G', 0.089472611853783468), 
      ('A', 0.1930724782107959), 
      ('T', 0.22132698721725386)], 
     [('C', 0.020962390607965918), 
      ('A', 0.026202988259957396), 
      ('G', 0.066380903591892068), 
      ('T', 0.07336836712788071)], 
     [('G', 0.0), 
      ('A', 0.10236420974570831), 
      ('C', 0.15354631461856247), 
      ('T', 0.29173799777526871)], 
     [('G', 0.027681850851852024), 
      ('C', 0.089966015268519078), 
      ('A', 0.089966015268519078), 
      ('T', 0.53287562889815143)], 
     [('A', 0.034165612000664765), 
      ('C', 0.06833122400132953), 
      ('G', 0.072601925501412631), 
      ('T', 0.28186629900548432)], 
     [('G', 0.0), 
      ('A', 0.037325935579058833), 
      ('C', 0.23328709736911771), 
      ('T', 0.72785574379164719)], 
     [('A', 0.017470244196759552), 
      ('C', 0.062892879108334396), 
      ('G', 0.094339318662501587), 
      ('T', 0.19916078384305891)], 
     [('G', 0.0), 
      ('A', 0.096447131567581681), 
      ('C', 0.15844885900388422), 
      ('T', 0.48223565783790845)], 
     [('G', 0.0), 
      ('A', 0.069291952024925829), 
      ('C', 0.20787585607477749), 
      ('T', 0.46425607856700307)], 
     [('G', 0.0), 
      ('A', 0.0), 
      ('C', 0.21713201856318373), 
      ('T', 1.1495224512168551)], 
     [('G', 0.0), 
      ('A', 0.048934292002649343), 
      ('T', 0.27263391258618919), 
      ('C', 0.42642740173737281)], 
     [('A', 0.0), 
      ('G', 0.053607190685875404), 
      ('C', 0.2054942309625224), 
      ('T', 0.69689347891638032)], 
     [('G', 0.0), 
      ('A', 0.0), 
      ('C', 0.31312908494534769), 
      ('T', 0.84220926295645249)], 
     [('G', 0.0), 
      ('C', 0.068079835765814778), 
      ('A', 0.068079835765814778), 
      ('T', 1.3207488138568066)], 
     [('G', 0.020257705570431345), 
      ('A', 0.020257705570431345), 
      ('C', 0.048618493369035232), 
      ('T', 0.055371061892512348)], 
     [('G', 0.0), 
      ('A', 0.076286510680262556), 
      ('C', 0.20538675952378382), 
      ('T', 0.34622339462580698)]]

輸出，用於`ALL_SCORE2' ：

希望的輸出：

如在notebook看到，xticklabels與字母不匹配。我希望能夠在xticks上應用offset_copy變換，以便字母的中心與蜱對齊。

來源

2017-03-05 rightskewed

你爲什麼要改造文本（GATC的）與屏幕座標，而不是軸座標？我認爲這會更容易，更有意義。 –

請小心張貼圖片？ –

讓你的問題完成，而不是讓人們跟隨你的鏈接。 –

我能夠通過使用屏幕要解決座標：

def draw_logo(all_scores, fontfamily='Arial', size=80): 
    mpl.rcParams['font.family'] = fontfamily 

    fig, ax = plt.subplots(figsize=(len(all_scores), 2.5)) 

    font = FontProperties() 
    font.set_size(size) 
    font.set_weight('bold') 

    #font.set_family(fontfamily) 

    ax.set_xticks(range(1,len(all_scores)+1))  
    ax.set_yticks(range(0,3)) 
    ax.set_xticklabels(range(1,len(all_scores)+1), rotation=90) 
    ax.set_yticklabels(np.arange(0,3,1))  
    seaborn.despine(ax=ax, trim=True) 

    trans_offset = transforms.offset_copy(ax.transData, 
             fig=fig, 
             x=1, 
             y=0, 
             units='dots') 

    for index, scores in enumerate(all_scores): 
     yshift = 0 
     for base, score in scores: 
     txt = ax.text(index+1, 
         0, 
         base, 
         transform=trans_offset, 
         fontsize=80, 
         color=COLOR_SCHEME[base], 
         ha='center', 
         fontproperties=font, 

        ) 
     txt.set_path_effects([Scale(1.0, score)]) 
     fig.canvas.draw() 
     window_ext = txt.get_window_extent(txt._renderer) 
     yshift = window_ext.height*score 
     trans_offset = transforms.offset_copy(txt._transform, 
               fig=fig, 
               y=yshift, 
               units='points') 
    trans_offset = transforms.offset_copy(ax.transData, 
              fig=fig, 
              x=1, 
              y=0, 
              units='points')  
plt.show()

例子：

Link to Jupyter Notebook

來源

2017-03-16 01:43:52 rightskewed

我建議不要直接在屏幕座標上工作，如果更改圖形大小或dpi，它會中斷。 – tacaswell

@tacaswell數字大小取決於圖案的長度。我想保持dpi不變。 – rightskewed

我建議在整個腳本中使用數據座標和單位座標。

gact.py
以給定比例繪製給定位置的字母的腳本。一個障礙是由TextPath創建的字母在相對位置（0,0）處具有其左下角，並且它們不跨越（1,1）的完整範圍。因此，我們需要將TextPath左移，以使字母的下部中心位於（0,0）處，並引入一個globscale縮放參數，這使得字母的高度單位爲1。不幸的是，這取決於正在使用的字體，所以對於不同的字體，人們必須再次調整x座標和globscale參數。

import matplotlib as mpl 
from matplotlib.text import TextPath 
from matplotlib.patches import PathPatch 
from matplotlib.font_manager import FontProperties 

fp = FontProperties(family="Arial", weight="bold") 
globscale = 1.35 
LETTERS = { "T" : TextPath((-0.305, 0), "T", size=1, prop=fp), 
      "G" : TextPath((-0.384, 0), "G", size=1, prop=fp), 
      "A" : TextPath((-0.35, 0), "A", size=1, prop=fp), 
      "C" : TextPath((-0.366, 0), "C", size=1, prop=fp) } 
COLOR_SCHEME = {'G': 'orange', 
       'A': 'red', 
       'C': 'blue', 
       'T': 'darkgreen'} 

def letterAt(letter, x, y, yscale=1, ax=None): 
    text = LETTERS[letter] 

    t = mpl.transforms.Affine2D().scale(1*globscale, yscale*globscale) + \ 
     mpl.transforms.Affine2D().translate(x,y) + ax.transData 
    p = PathPatch(text, lw=0, fc=COLOR_SCHEME[letter], transform=t) 
    if ax != None: 
     ax.add_artist(p) 
    return p

運行的代碼

import matplotlib.pyplot as plt 
import gact 

fig, ax = plt.subplots(figsize=(10,3)) 

all_scores = ALL_SCORES2 
x = 1 
maxi = 0 
for scores in all_scores: 
    y = 0 
    for base, score in scores: 
     gact.letterAt(base, x,y, score, ax) 
     y += score 
    x += 1 
    maxi = max(maxi, y) 

plt.xticks(range(1,x)) 
plt.xlim((0, x)) 
plt.ylim((0, maxi)) 
plt.tight_layout()  
plt.show()

來源

2017-03-06 17:20:18 ImportanceOfBeingErnest

這看起來不錯！你怎麼決定'TextPath'的座標？ – rightskewed

我編輯了答案，希望能夠更清楚地瞭解座標。如果您需要更高的準確度，則可能需要更加準確地測量字母的高度，以在「globscale」參數中進行說明。 – ImportanceOfBeingErnest

對於'TextPath'，這是不是很準確：我發現每個字母都需要一個不同的'globscale'參數來保持相同的高度，所以我不會使用這個函數。科學論文... – Cokes

matplotlib中的序列標識：aligning xticks

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