在jupyter笔记本中用不等分热图绘制交互式图形

Question

我试图在jupyter笔记本上绘制一个交互式树状图，在jupyter笔记本上使用不等热图，使用将看上去像这个的package。

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我的示例数据dataHeat_arr是numpy.ndarray，它有75行(称为S0到S74)和100列(代谢物称为M0直到M99)，并可在链接中使用。

在链接中有3个csv文件。

1. dataHeat_arr.csv - numpy.ndarray 75*100
2. name_molec.csv -名为M0，M1，.直到M99
3. Samplenum.csv -名为S0，S1，.直到S74

我根据来自她的例子编写了代码，并做了一些更改，因为我的热垫是不平衡的。

也尝试过questoins 聚类热图(带树状图)/Python

我不知道我在做什么，因为最终的数字是错过了热图。只有在用等量热图绘制时，我才能用树状图绘制热图。

她是我的密码。

进口包装：

import plotly.figure_factory as ff
import numpy as np
np.random.seed(1)
import pandas as pd
import numpy as np
import string 
from itables import init_notebook_mode
from itables import show
import cimcb_lite as cb
import plotly.graph_objects as go
init_notebook_mode(all_interactive=True)

通过创建上面的树状图：来初始化图形

# name the samples S0 till S74

# Samplenum & name_molec are csv files in the link of Github and should be treated as lists
labels = Samplenum
dataHeat_arr_t= np.transpose(dataHeat_arr)

# Initialize figure by creating upper dendrogram
fig = ff.create_dendrogram(dataHeat_arr, orientation='bottom', labels=labels)

# fig = ff.create_dendrogram(dataHeat_arr_t, orientation='bottom', labels=name_molec[:100] ) ,labels=name_molec[:100]

for i in range(len(fig['data'])):
    fig['data'][i]['yaxis'] = 'y2'

然后创建侧Dendrogram:

# Create Side Dendrogram

dendro_side = ff.create_dendrogram(dataHeat_arr_t, orientation='right' ,labels=name_molec[:100])
# dendro_side = ff.create_dendrogram(dataHeat_arr, orientation='right', labels=labels)
for i in range(len(dendro_side['data'])):
    dendro_side['data'][i]['xaxis'] = 'x2'
     
# Add Side Dendrogram Data to Figure
for data in dendro_side['data']:
    fig.add_trace(data)

创建热图：

heatmap = [
    go.Heatmap(
        x = name_molec[:100],
        y =labels ,
        z = dataHeat_arr,
        colorscale = 'Cividis'
    )
]

向图中添加热图数据：

for data in heatmap:
    fig.add_trace(data)

现在的布局：

# Edit Layout
fig.update_layout({'width':1500, 'height':750,
                         'showlegend':False, 'hovermode': 'closest',
                         })
# Edit xaxis
fig.update_layout(xaxis={'domain': [.15, 1],
                                  'mirror': False,
                                  'showgrid': False,
                                  'showline': False,
                                  'zeroline': False,
                                  'ticks':""})

# Edit xaxis2
fig.update_layout(xaxis2={'domain': [0, .15],
                                   'mirror': False,
                                   'showgrid': False,
                                   'showline': False,
                                   'zeroline': False,
                                   'showticklabels': False,
                                   'ticks':""})

# Edit yaxis
fig.update_layout(yaxis={'domain': [0, .85],
                                  'mirror': False,
                                  'showgrid': False,
                                  'showline': False,
                                  'zeroline': False,
                                  'showticklabels': False,
                                  'ticks': ""
                        })

# Edit yaxis2
fig.update_layout(yaxis2={'domain':[0.852, 0.975],
                                   'mirror': False,
                                   'showgrid': False,
                                   'showline': False,
                                   'zeroline': False,
                                   'showticklabels': False,
                                   'ticks':""})

fig.show()

出于某种原因，情节看起来是这样的：

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任何想法/暗示都将是有用的和见效的！

Answer 1

在y轴和x-aix上用树状图绘制热图的正确代码：

通过创建上面的树状图：来初始化图形

Samplenum = ["S" + str(x) for x in idx]
labels = Samplenum
dataHeat_arr_t= np.transpose(dataHeat_arr)
# Initialize figure by creating upper dendrogram

# The line below was changed comparing to my question 
fig = ff.create_dendrogram(dataHeat_arr_t, orientation='bottom', labels=name_molec[:99] )


for i in range(len(fig['data'])):
    fig['data'][i]['yaxis'] = 'y2'

创建侧树图

# The line below was changed as well comparing to my question 
dendro_side = ff.create_dendrogram(dataHeat_arr, orientation='right', labels=["S" + str(x) for x in idx])
for i in range(len(dendro_side['data'])):
    dendro_side['data'][i]['xaxis'] = 'x2'
    
    
# Add Side Dendrogram Data to Figure
for data in dendro_side['data']:
    fig.add_trace(data)

创建热图：

heatmap = [
    go.Heatmap(
        x = name_molec[:99],
        y =labels ,
        z = dataHeat_arr,
        colorscale = 'Cividis'
    )
]

这4行是新的(我的问题中没有)：

heatmap[0]['x'] = fig['layout']['xaxis']['tickvals']
heatmap[0]['y'] = dendro_side['layout']['yaxis']['tickvals']


# to tickes text on y-axis as well
fig['layout']['yaxis']['ticktext'] = np.asarray(labels)
fig['layout']['yaxis']['tickvals'] = np.asarray(dendro_side['layout']['yaxis']['tickvals'])

大多数布局代码保持不变，但:showticklabels': True

# Edit yaxis
fig.update_layout(yaxis={'domain': [0, .7],
                                  'mirror': False,
                                  'showgrid': False,
                                  'showline': False,
                                  'zeroline': False,
                                  'showticklabels': True,
                                  'ticks': ""
                        })

输出结果看上去更像我问题开头的图片。

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