python - sequence logos in matplotlib: aligning xticks

4
votes

I am trying to draw sequence logos using matplotlib. The entire code is available on gist

The relevant portion is:

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)]]

Output for `ALL_SCORE2': enter image description here

Desired output: enter image description here

As seen in the notebook, the xticklabels do not align well with the alphabets. I would want to be able to apply offset_copy transforms on the xticks too, so that the centers of the alphabets align with the ticks.

Update

I have wrapped this up as a python package in pyseqlogo

3
pythonmatplotlibdna-sequence
Why are you transforming the text (the GATC's) with screen coordinates instead of axis coordinates? I'd think that would be easier and make more sense. - Douglas Dawson
Care to post a picture please? - Mad Physicist
Make your question complete instead of making people follow your links. - Mad Physicist

3 Answers

8
votes

I would suggest to work in data coordinates and unit coordinates throughout the script.

gact.py
Script to plot a letter at a given position with a given scale. One obstacle is that the letters created by TextPath have their lower left corner at relative position (0,0) and that they don't span the complete range up to (1,1). We therefore need to shift the TextPath to the left such that the lower center of the letter is at (0,0) and introduce a globscale scaling parameter, which makes the letter 1 unit in height. Unfortunately this depends on the font being used, so for a different font, one has to adapt the x coordinate and the globscale parameter again.

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

running code

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()

enter image description here

1
votes

I simplified the code to make it generalizable to DPI/screen coordinates. The major change is that it draws the first character and then measures its screen width/height and then uses those parameters for the rest.

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)

Sample output

1
votes

I was able to workaround by using the screen coordinates:

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()

Examples:

enter image description here

enter image description here

Link to Jupyter Notebook

pyseqlogo

dmslogo