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How to use clustermap in seaborn

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by vinitha@openweaver.com dot icon Updated: Sep 6, 2023

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A clustered heatmap, also known as a "clustermaps". It is a specific type of data visualization available in Seaborn. 

 

A seaborn clustermap combines a heatmap with hierarchical clustering and dendrograms. It helps you explore patterns and relationships in your data. A hierarchically clustered heatmap is a type of seaborn heatmap. 

 

Using hierarchical clustering, we reorder a matrix's rows and columns. This helps in visually identifying patterns and relationships in the data. Perform the clustering on your data using Scipy's linkage method and dendrogram.  

   

A clustering algorithm's colors data points on a scatter plot. It helps to identify clusters within the data values. Seaborn provides the clustering scattered plot used to create scatter plots with colormap.  

   

When you use Seaborn's clustermap function, you can specify the column names to use in the plot. It provides the appropriate parameters. The clustermap function works with pandas DataFrames column names. It allows you to use column labels to visualize the data structure better.  

   

In conclusion, Seaborn's clustermap function is a versatile tool. It helps explore and analyze structured data visually. You can use hierarchical clustering to understand patterns and relationships in your data. You can also use heatmap visualization and dendrograms. Clustermap can assist with data preprocessing, pattern recognition, and exploratory data analysis. It helps you gain insights and make informed decisions using your data.  

Fig: Preview of the output that you will get on running this code from your IDE

Code

In this solution we are using seaborn library

Adding seaborn clustermap to figure with other plots

PythondotLines of Code : 23dotLicense : Strong Copyleft (CC BY-SA 4.0)

Dependent Libraries : 
import seaborn as sns; sns.set(color_codes=True)
import matplotlib.pyplot as plt
import matplotlib.gridspec

iris = sns.load_dataset("iris")
species = iris.pop("species")

lut = dict(zip(species.unique(), "rbg"))
row_colors = species.map(lut)

#First create the clustermap figure
g = sns.clustermap(iris, row_colors=row_colors, figsize=(13,8))
# set the gridspec to only cover half of the figure
g.gs.update(left=0.05, right=0.45)

#create new gridspec for the right part
gs2 = matplotlib.gridspec.GridSpec(1,1, left=0.6)
# create axes within this new gridspec
ax2 = g.fig.add_subplot(gs2[0])
# plot boxplot in the new axes
sns.boxplot(data=iris, orient="h", palette="Set2", ax = ax2)
plt.show()

Instructions

Follow the steps carefully to get the output easily.


  1. Download and Install the PyCharm Community Edition on your computer.
  2. Open the terminal and install the required libraries with the following commands.
  3. Install seaborn - pip install seaborn
  4. Create a new Python file on your IDE.
  5. Copy the snippet using the 'copy' button and paste it into your python file.
  6. Run the current file to generate the output.


I hope you found this useful.


I found this code snippet by searching for ' Adding seaborn clustermap to figure with other plots ' in Kandi. You can try any such use case!

Environment tested

I tested this solution in the following versions. Be mindful of changes when working with other versions.

  1. PyCharm Community Edition 2023.1
  2. The solution is created in Python 3.11.1 Version
  3. Seaborn 1.0.7 Version


Using this solution, we can able to use clustermap in seaborn with simple steps. This process also facilities an easy way to use, hassle-free method to create a hands-on working version of code which would help us to use clustermap method in seaborn.

Dependency library

seabornby mwaskom

Python doticonstar image 10797 doticonVersion:v0.12.2doticon
License: Permissive (BSD-3-Clause)

Statistical data visualization in Python

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            seabornby mwaskom

            Python doticon star image 10797 doticonVersion:v0.12.2doticon License: Permissive (BSD-3-Clause)

            Statistical data visualization in Python
            Support
              Quality
                Security
                  License
                    Reuse

                      You can search for any dependent library on kandi like ' Seaborn '.

                      FAQ:  

                      1. How can one use Seaborn's Clustermap to explore data quickly?  

                      Seaborn's clustermap is an excellent tool for quickly exploring your data. You can use it to view patterns and relationships in a clustered heatmap.

                       

                      Here's how you can use clustermap to explore your data quickly:  

                      • Load or Prepare Data  
                      • Create a Clustermap  
                      • Observe Dendrograms  
                      • Analyze Heatmap  
                      • Explore Relationships  
                      • Identify Outliers  

                        

                      2. How does hierarchical clustering work in Seaborn's Clustermap?  

                      Seaborn's clustermap employs hierarchical clustering to organize the data in a clustered heatmap. Here's a breakdown of how hierarchical clustering works within clustermap:   

                      • Distance Computation  
                      • Hierarchical Linkage  
                      • Hierarchical Clustering  
                      • Dendrograms  
                      • Reordering Rows and Columns  

                       

                      3. Can I plot a matrix with Seaborn's Clustermap, or is that impossible?  

                      Yes, you can certainly plot a matrix using Seaborn's clustermap function. Plotting a matrix is one of the primary purposes of clustermap. The function takes a matrix and creates a heatmap with dendrograms to show the hierarchy.  

                       

                      4. What types of colormap are available when using Seaborn's Clustermap?  

                      Seaborn's clustermap function provides a variety of colormaps. Users customize the appearance of the heatmap within the clustered visualization.  

                       

                      Here's a selection of available colormaps:  

                      • Sequential Colormaps  
                      • Diverging Colormaps  
                      • Qualitative Colormaps  
                      • Custom Colormaps  

                       

                      5. Can the seaborn cluster map function take a precomputed linkage matrix as input?  

                      Seaborn's clustermap does not support providing a precomputed linkage matrix as an input. The clustermap function performs hierarchical clustering using the given data matrix. It calculates pairwise distances and builds the linkage matrix itself.  

                       

                      Here is a basic guide on using a precomputed linkage matrix for visualization. 

                      • Use Scipy to Compute Linkage  
                      • Create Dendrogram  
                      • Reorder Data and Heatmap  

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