Pheatmap in R: Setting Fixed Limits of Heatmap Legend

Question

I am working in R with the pheatmap library. I am creating heatmaps for different timepoints for the same population, so I want the legend scale to be fixed (from -2 to 2) for each heatmap so they can be easily compared. Then, values that are outside of that range would be set to the color of either -2 or 2.

I've tried to set a fixed range by using the legend_break and legend_labels options, but they only change the labels on the legend, not the actual scale limits themselves.

# Set Legend Limits
legend_breaks <- seq(-2, 2, length.out = 21)  
legend_labels <- c("-2", rep("", 4), "-1", rep("", 4), "0", 
                   rep("", 4), "1", rep("", 4), "2")  

# Plot Heat Map
pheatmap(temp_m[,8:ncol(temp_m)],
    scale="column",
    annotation_colors = ann_colors,
    color=colorRampPalette(c("navy", "white", "red"))(20),
    main="Temp",
    cluster_rows = FALSE,
    cluster_cols = FALSE,
    show_rownames = FALSE,
    gaps_row = gaps,
    angle_col = 90,
    border_color = "grey",
    legend_breaks = legend_breaks,
    legend_labels = legend_labels,
    annotation_row = rows,
    # annotation_legend = TRUE,
    # annotation_names_row = TRUE,
    fontsize=11, cellwidth=10, cellheight=10)

Answer 1

I just had a solution about how to get a same scale in the legend across different heatmaps made by pheatmap package in R.

In your case, you can try add:

color = colorRampPalette(c("navy", "white", "red"))(20)

breaks = c( -2, -1.8, -1.6, -1.4, -1.2, -1.0, -0.8, -0.6, -0.4, -0.2, 0, 0.2, 0.4, 0.6, 0.8, 1, 1.2, 1.4, 1.6, 1.8, 2.0, 2.2)

If you scale the legend from -10 to 10, and the number of color increase from 20 to 50, the sequence of numbers in breaks could be have interval of 0.4 (20/50 = 0.4). The point is that the number of the sequence number in breaks is same to the number of the color.

pheatmap(temp_m[,8:ncol(temp_m)],
    scale="column",
    annotation_colors = ann_colors,
    color=color, breaks = breaks
    main="Temp",
    cluster_rows = FALSE,
    cluster_cols = FALSE,
    show_rownames = FALSE,
    gaps_row = gaps,
    angle_col = 90,
    border_color = "grey",
    legend_breaks = legend_breaks,
    legend_labels = legend_labels,
    annotation_row = rows,
    # annotation_legend = TRUE,
    # annotation_names_row = TRUE,
    fontsize=11, cellwidth=10, cellheight=10)