python里xticks_python – matplotlib中的序列标识：对齐xticks

我正在尝试使用matplotlib绘制

sequence logos.

整个代码可在

gist获得

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

我在pyseqlogo将它包装成python包

最佳答案 我建议在整个脚本中使用数据坐标和单位坐标.

gact.py

用给定比例在给定位置绘制字母的脚本.一个障碍是TextPath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移到左侧,使得字母的下部中心位于(0,0)并引入一个全球缩放比例参数,这使得字母1的单位为高度.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globscale参数.

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

运行代码

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()