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The post The pheatmap function in R appeared first on Data Science Tutorials

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The pheatmap function in R, the pheatmap function gives you more control over the final plot than the standard base R heatmap does.

A numerical matrix holding the values to be plotted can be passed.

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```# install.packages("pheatmap")
library(pheatmap)
# Data
set.seed(123)
m <- matrix(rnorm(200), 10, 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)
# Heat map
pheatmap(m)```

Normalization

If the matrix’s values are not normalized, you can use the scale parameter to normalize them by either the rows (“row”) or the columns (“column”) of the matrix.

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```m <- matrix(rnorm(200), 10, 10)
colnames(m) <- paste("Col", 1:10)
rownames(m) <- paste("Row", 1:10)
# Heat map
pheatmap(m, scale = "column")```

Values

Display_numbers = TRUE causes the values for each cell to be displayed. The text’s size and colour can both be changed.

```pheatmap(m,
display_numbers = TRUE,
number_color = "black",
fontsize_number = 8)```

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Number of clusters

With kmeans_k, the number of clusters can be altered. If there aren’t enough clusters, you can enlarge the cells using cellheight or cellwidth.

`pheatmap(m, kmeans_k = 3, cellheight = 50)`

Remove rows dendrogram

`pheatmap(m, cluster_rows = FALSE)`

Remove columns dendrogram

`pheatmap(m, cluster_cols = FALSE)`

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Remove dendrograms

```pheatmap(m,
cluster_cols = FALSE,
cluster_rows = FALSE)```

Border color

`pheatmap(m, border_color = "black")`

Color palette

`pheatmap(m, color = hcl.colors(50, "BluYl"))`

Legend breaks

`heatmap(m, legend_breaks = c(-2, 0, 2))`

Legend labels

```pheatmap(m,
legend_breaks = c(-2, 0, 2),
legend_labels = c("Low", "Medium", "High"))```

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Remove the legend

`pheatmap(m, legend = FALSE)`

The post The pheatmap function in R appeared first on Data Science Tutorials

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