I am currently trying to create a very hight but narrow dendrogram, without any margins in top or bottom. The problem is that, as the dendrogram becomes higher, there appears a strange gap between the dendrogram and the top of its container, even when I explicitly set margin and padding to 0.
Down below there is a code example to create a dendrogram in which this strange gap can be seen. Do you know why this might be happening?
Thank you in advance
import matplotlib
matplotlib.use('Agg')
import pandas as pd
from plotly.figure_factory import create_dendrogram
from plotly.offline import plot,init_notebook_mode, plot
import numpy as np
from scipy.cluster.hierarchy import linkage, fcluster
height = 3000
width = 600
clusters = 10
dend_matrix = np.random.rand(200,2)
filename = "dummy_dendrogram.html"
# Define linkage function (we'll be using the default one for plotly).
linkagefun=lambda x: linkage(x, 'complete')
# Create color scale from the "category20" color scale. Not working because color_scale plotly option is inoperative
colors_category20 = ['rgb(31, 119, 180)', 'rgb(174, 199, 232)', 'rgb(255, 127, 14)', 'rgb(255, 187, 120)', 'rgb(44, 160, 44)', 'rgb(152, 223, 138)', 'rgb(214, 39, 40)', 'rgb(255, 152, 150)', 'rgb(148, 103, 189)', 'rgb(197, 176, 213)', 'rgb(140, 86, 75)', 'rgb(196, 156, 148)', 'rgb(227, 119, 194)', 'rgb(247, 182, 210)', 'rgb(127, 127, 127)', 'rgb(199, 199, 199)', 'rgb(188, 189, 34)', 'rgb(219, 219, 141)', 'rgb(23, 190, 207)', 'rgb(158, 218, 229)']
colors = colors_category20[0:clusters]
# Setting figures
fig = create_dendrogram(
dend_matrix,
orientation='right',
linkagefun=linkagefun,
)
fig['layout'].update({
'width':width,
'height':height,
})
fig['layout']['margin'].update({
'r' : 300,
'l' : 50,
't' : 0,
'b' : 0,
'pad' : 0,
'autoexpand' : False,
})
fig['layout']['xaxis'].update({
'showline': False,
'showticklabels': False,
'ticks' : '',
'fixedrange' : True,
'automargin' : False
})
fig['layout']['yaxis'].update({
'side' : 'right',
'showline': False,
'ticks' : '',
'tickfont' : {
'size' : 15,
'color' : 'white'
},
'fixedrange' : True,
'automargin' : False
})
# Taking order for plot rows
dendro_leaves = fig['layout']['yaxis']['ticktext']
# Writing dendrogram on file
plot(fig, auto_open= True, filename=filename, config={
"displayModeBar": "hover",
"modeBarButtons": [["toImage"]]
})
