[Python] Heatmap (seaborn) doesn't show all Ylabels [duplicate]

My heatmap doesn't want to show all Ylabels.

This is the plot

And this is the code

import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt

# Load the dataset from a file (e.g., 'data.csv')
file_path = 'data.csv' # Replace with your file path
df = pd.read_csv(file_path, sep='\t')

# Convert the "VAF from Genotyping" column to numeric after removing the percentage sign
df['VAF from Genotyping'] = df['VAF from Genotyping'].str.rstrip('%').astype(float)

# Sort the dataframe by "VAF from Genotyping" in descending order
df_sorted = df.sort_values(by='VAF from Genotyping', ascending=False)

# Modify Sample-Run labels to include #Reads in BAM and VAF from Genotyping
df_sorted["Sample-Run"] = df_sorted["Sample-Run"] + " (" + df_sorted["#Reads in BAM"].astype(str) + " Reads, " + df_sorted["VAF from Genotyping"].astype(str) + "% VAF)"

# Convert detection status to binary
threshold_cols = ["6K", "10K", "15K", "20K", "25K", "35K"]
df_binary = df_sorted[threshold_cols].replace({"No Mutation Detected": 0, "Variant": 1})

# Ensure binary index matches Sample-Run
df_binary.index = df_sorted["Sample-Run"]


print(len(df_binary))

# --- Heatmap Plot ---
plt.figure(figsize=(12, 8))
sns.heatmap(df_binary, cmap="Blues", annot=True, cbar=True, fmt="d")
plt.title("Mutation Detection Matrix Across Thresholds", fontsize=14)
plt.xlabel("Read Thresholds", fontsize=12)
plt.ylabel("Wnumber-RunID Read VAF", fontsize=12)

plt.gca().set_yticklabels(plt.gca().get_yticklabels(), fontsize=10)


# Save heatmap
heatmap_file = "detection_matrix_with_metadata.png"
plt.tight_layout()
plt.savefig(heatmap_file)
plt.close() # Close the figure

# Save the sorted dataset to a new file
output_file = 'sorted_data_with_metadata.csv'
df_sorted.to_csv(output_file, index=False, sep='\t')

# Confirmation
print(f"Sorted data saved to '{output_file}'")
print(f"Heatmap saved as '{heatmap_file}'")


The print(len(df_binary)) showed me that the heatmap function takes 54 elements and I can see that in the number of 0s in the first column of the heatmap. However, the plot only show around 27 Ylabels. Why???

Continue reading...