Customizing colors¶

Using link_color_func¶

Coloring based on linkage ID¶

Colors are controlled via link_color_func parameter of idd.create_dendrogram function. To customize colors, pass a callable that returns an appropriate color for a given linkage ID as link_color_func (this function also receives clustering data container which is not required in this example).

For example, to give each link/node a different color, one could do this:

In [3]:

#instantiate idendrogram object and pass clustering data
idd = idendrogram.idendrogram()
idd.set_cluster_info(cl_data)

#mapping from linkage_id to hex format color string 
# using an arbitrary id -> rbg mapping
node_painter = lambda _, linkage_id: '#{:02x}{:02x}{:02x}'.format(
    linkage_id % 255, 
    (linkage_id * linkage_id) % 255,  
    linkage_id % 3 * linkage_id % 10
)

#create a dendrogram object
dendrogram = idd.create_dendrogram(link_color_func=node_painter)
to_altair(dendrogram=dendrogram, height=200, width=629)

#instantiate idendrogram object and pass clustering data idd = idendrogram.idendrogram() idd.set_cluster_info(cl_data) #mapping from linkage_id to hex format color string # using an arbitrary id -> rbg mapping node_painter = lambda _, linkage_id: '#{:02x}{:02x}{:02x}'.format( linkage_id % 255, (linkage_id * linkage_id) % 255, linkage_id % 3 * linkage_id % 10 ) #create a dendrogram object dendrogram = idd.create_dendrogram(link_color_func=node_painter) to_altair(dendrogram=dendrogram, height=200, width=629)

Out[3]:

Coloring based on cluster ID¶

Often, dendrograms are colored so that all nodes/links that belong to a cluster are painted the same color. This requires knowledge of how to map linkage_id to clustering information. A convenience function idendrogram.callbacks.link_painter is available that does the mapping under the hood - all you need to provide is a list of cluster IDs and corresponding colors, and a color to be used for merged clusters.

In [4]:

cluster_painter = idendrogram.callbacks.link_painter(
    colors={
        1: 'red',
        2: 'blue',
        3: 'green',
    }, 
    above_threshold='black'
)

cluster_painter = idendrogram.callbacks.link_painter( colors={ 1: 'red', 2: 'blue', 3: 'green', }, above_threshold='black' )

In [5]:

#create a dendrogram object
dendrogram = idd.create_dendrogram(link_color_func=cluster_painter)
to_altair(dendrogram=dendrogram, height=200, width=629)

#create a dendrogram object dendrogram = idd.create_dendrogram(link_color_func=cluster_painter) to_altair(dendrogram=dendrogram, height=200, width=629)

Out[5]:

Changing default text colors¶

Default colors of nodes and links are defined in idendrogram.containers.ClusterNode and idendrogram.containers.ClusterLink. You can either set different defaults in advance or post-process after the dendrogram is created.

Setting different defaults¶

The easiest way to change defaults is by defining a new dataclass with appropriate values and passing it to the idendrogram() constructor.

In [6]:

from idendrogram.containers import ClusterNode
from dataclasses import dataclass

@dataclass
class MyNode(ClusterNode):
    labelcolor: str = 'pink'
    edgecolor: str = 'orange'
    fillcolor: str = 'yellow'

idd = idendrogram.idendrogram(node_factory=lambda x:  MyNode(**x))
idd.set_cluster_info(cl_data)

# make nodes black-ish otherwise
node_painter = lambda _, linkage_id: '#{:02x}{:02x}{:02x}'.format(
    0, 
    0,
    (linkage_id) % 255,  
)

#create a dendrogram object
dendrogram = idd.create_dendrogram(link_color_func=node_painter)
to_altair(dendrogram=dendrogram, height=200, width=629)

from idendrogram.containers import ClusterNode from dataclasses import dataclass @dataclass class MyNode(ClusterNode): labelcolor: str = 'pink' edgecolor: str = 'orange' fillcolor: str = 'yellow' idd = idendrogram.idendrogram(node_factory=lambda x: MyNode(**x)) idd.set_cluster_info(cl_data) # make nodes black-ish otherwise node_painter = lambda _, linkage_id: '#{:02x}{:02x}{:02x}'.format( 0, 0, (linkage_id) % 255, ) #create a dendrogram object dendrogram = idd.create_dendrogram(link_color_func=node_painter) to_altair(dendrogram=dendrogram, height=200, width=629)

Out[6]:

Monochrome dendrograms¶

Note that nodes are still colored using the default link_color_func parameter, so if you want to have a completely single-colored dendrogram version, you need to change that, too.

In [7]:

@dataclass
class MonochromeNode(ClusterNode):
    labelcolor: str = 'white'
    edgecolor: str = 'grey'
    fillcolor: str = 'grey'

idd = idendrogram.idendrogram(node_factory=lambda x:  MonochromeNode(**x))
idd.set_cluster_info(cl_data)

# make nodes black-ish otherwise
grey_painter = lambda _, __: "grey"

#create a dendrogram object
dendrogram = idd.create_dendrogram(link_color_func=grey_painter)
to_altair(dendrogram=dendrogram, height=200, width=629)

@dataclass class MonochromeNode(ClusterNode): labelcolor: str = 'white' edgecolor: str = 'grey' fillcolor: str = 'grey' idd = idendrogram.idendrogram(node_factory=lambda x: MonochromeNode(**x)) idd.set_cluster_info(cl_data) # make nodes black-ish otherwise grey_painter = lambda _, __: "grey" #create a dendrogram object dendrogram = idd.create_dendrogram(link_color_func=grey_painter) to_altair(dendrogram=dendrogram, height=200, width=629)

Out[7]:

Coloring in post-processing¶

You can also redefine color values or each node and link separately after the dendrogram has been created.

In [8]:

dendrogram = idd.create_dendrogram()
for i, n in enumerate(dendrogram.nodes):
    if i % 2 == 0:
        n.edgecolor = 'red'
        n.fillcolor = 'red'
        n.labelcolor = 'lightgrey'
    else:       
        n.edgecolor = 'lightgrey'
        n.fillcolor = 'lightgrey'
        n.labelcolor = 'red'
for i, l in enumerate(dendrogram.links):
    if i % 2 == 0:
        l.fillcolor = 'blue'        
    else:       
        l.fillcolor = 'green'

to_altair(dendrogram=dendrogram, height=200, width=629)

dendrogram = idd.create_dendrogram() for i, n in enumerate(dendrogram.nodes): if i % 2 == 0: n.edgecolor = 'red' n.fillcolor = 'red' n.labelcolor = 'lightgrey' else: n.edgecolor = 'lightgrey' n.fillcolor = 'lightgrey' n.labelcolor = 'red' for i, l in enumerate(dendrogram.links): if i % 2 == 0: l.fillcolor = 'blue' else: l.fillcolor = 'green' to_altair(dendrogram=dendrogram, height=200, width=629)

Out[8]: