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
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3 个答案:
答案 0 :(得分：6)
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 
答案 1 :(得分：1)
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)
答案 2 :(得分：0)
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：
- 我写了这段代码，但我无法理解我的错误
- 我无法从一个代码实例的列表中删除 None 值，但我可以在另一个实例中。为什么它适用于一个细分市场而不适用于另一个细分市场？
- 是否有可能使 loadstring 不可能等于打印？卢阿
- java中的random.expovariate()
- Appscript 通过会议在 Google 日历中发送电子邮件和创建活动
- 为什么我的 Onclick 箭头功能在 React 中不起作用？
- 在此代码中是否有使用“this”的替代方法？
- 在 SQL Server 和 PostgreSQL 上查询，我如何从第一个表获得第二个表的可视化
- 每千个数字得到
- 更新了城市边界 KML 文件的来源？