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Question

我正在尝试使用matplotlib绘制sequence logos。整个代码可在gist

上找到

相关部分是：

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)]]

“ALL_SCORE2”的输出：

期望的输出：

如notebook所示，xticklabels与字母表不能很好地对齐。我希望能够在xticks上应用offset_copy变换，以便字母的中心与刻度线对齐。

更新

我已将其作为python包裹在pyseqlogo

中

Answer 1

我建议在整个脚本中使用数据坐标和单位坐标。

<强> gact.py
用给定比例在给定位置绘制字母的脚本。一个障碍是public class ChatModel { private String id; private String user; private String username; private String userphoto; private boolean send; private boolean delivered; private boolean seen; private boolean isEmji; private String userModel; private String message; private String timeStamp; private FileModel file; private MapModel mapModel; public ChatModel() { } public ChatModel(String senderID, String message, String timeStamp, FileModel file, boolean send, boolean delivered , boolean seen ,String ID , String username , String userphoto , Boolean isEmji) { this.userModel = senderID; this.message = message; this.timeStamp = timeStamp; this.file = file; this.send = send; this.id = ID; this.username = username; this.userphoto = userphoto; this.isEmji = isEmji; this.delivered = delivered; this.seen = seen; } public ChatModel(String senderID, String timeStamp, MapModel mapModel, boolean send, boolean delivered , boolean seen , String ID , String username , String userphoto , Boolean isEmji) { this.userModel = senderID; this.timeStamp = timeStamp; this.mapModel = mapModel; this.send = send; this.id = ID; this.username = username; this.userphoto = userphoto; this.isEmji = isEmji; this.delivered = delivered; this.seen = seen; } ....创建的字母的左下角位于相对位置（0,0），并且它们不会跨越整个范围直到（1,1）。因此，我们需要将TextPath向左移动，使得字母的下部中心位于（0,0）并引入final ListUserFirebaseAdapter firebaseAdapter = new ListUserFirebaseAdapter(mFirebaseDatabaseReference.child("users/" + id + "/Chats/").orderByChild("lastTimeStamp").getRef(), name, id , getActivity() ,this , getContext()); rvListMessage.setAdapter(firebaseAdapter);缩放参数，这使得字母1的高度为单位。不幸的是，这取决于所使用的字体，因此对于不同的字体，必须再次调整x坐标和TextPath参数。

globscale

正在运行的代码

globscale

Answer 2

我简化了代码，使其可以通用化为DPI /屏幕坐标。主要的变化是先绘制第一个字符，然后测量其屏幕宽度/高度，然后将这些参数用于其余字符。

from matplotlib.patheffects import RendererBase
from matplotlib.transforms import offset_copy
from matplotlib.patches import Rectangle

class Scale(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)

iupac = "XACMGRSVTWYHKDBN"

iupac_colors = ['black'] * 16
iupac_colors[1<<0] = 'blue'
iupac_colors[1<<1] = 'red'
iupac_colors[1<<2] = 'green'
iupac_colors[1<<3] = 'gold'     

fig, ax = plt.subplots()
fig.set_size_inches(4, 1)


w=25
ax.set_xlim(0, w)

xoffset=int((w-pwm.shape[1])/2)

wscale=1
for i in range(pwm.shape[1]):
    yshift = 0
    for j in range(4):
        base=iupac[(1<<j)]
        color=iupac_colors[(1<<j)]
        scale=pwm[j, i]

        t = ax.text(i+xoffset, yshift, base, ha='left', va='baseline', color=color, fontsize=80, family='monospace', weight='bold')

        if i==0 and j==0:
            fig.canvas.draw()
            ext = t.get_window_extent(t._renderer)

            x0, x1, y0, y1 = ext.x0, ext.x1, ext.y0, ext.y1
            nx0, ny0 = ax.transData.inverted().transform((x0, y0))
            nx1, ny1 = ax.transData.inverted().transform((x1, y1))

            wscale=1.0/(nx1-nx0)
            hscale=1.0/(ny1)
            height=ext.height

        t.set_path_effects([Scale(wscale, scale*hscale)])

        w=0
        h=(height)*scale*hscale

        x, y = fig.transFigure.inverted().transform((w, h))

        yshift += y

ax.set_xticks(np.arange(xoffset, xoffset+pwm.shape[1])+0.5)
ax.set_xticklabels(np.arange(pwm.shape[1])+1)
sns.despine(ax=ax)

Answer 3

我可以使用屏幕坐标解决方法：

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()

示例：

Link to Jupyter Notebook

matplotlib中的序列标识：对齐xticks

更新

3 个答案: