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Has anyone tried absence or presence heatmap ? (Or suggestion)

I have this kind of data (0=absence, 1=presence) with 4 groups, 21 samples as below.

enter image description here

As appeared in the excel, the 1 could appear as the color that represent the group (presence), how can I draw that information in heatmap using R ?

If anyone has similar experience of visualization, please leave me any recommendation for it.

  • Maybe there could be better way to represent the group and presence of the taxa in each samples with visualization.

Any code or comment for the heatmap visualization would be greatly appreciated !!

r absence heatmap grouping
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updated by KABILAN • KABILAN • written by ohtang7 • ohtang7

Just FYI, rows are 4 groups and columns are 21 samples.

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written by ohtang7 • ohtang7

1 answer 

library(ComplexHeatmap)

df1 <- df[,-2] #Change 'df' into your respective dataset
rownames(df1) <- df1$Index
df1 <- df1[,-1]

# Define a color scheme for binary data (0 and 1)
binary_colors <- c("0" = "blue", "1" = "red")

# Create the heatmap
Heatmap(as.matrix(df1), 
        name = "Presence", 
        col = binary_colors, 
        column_title = "Samples", 
        row_title = "Taxa", 
        show_column_names = TRUE, 
        show_row_names = FALSE,
        cluster_columns = FALSE,  # Disable clustering for clarity
        cluster_rows = FALSE)  # Disable clustering for clarity

You can try this R script. Change df into your respective dataset.

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written by KABILAN • KABILAN

What a nice suggestion ! I will try to use ComplexHeatmap library to conduct it. I didn't even know the package. Thank you very much.

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written by ohtang7 • ohtang7

Welcome. You can check the ComplexHeatmap manual in https://github.com/jokergoo/ComplexHeatmap.

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written by KABILAN • KABILAN

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