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Heatmap with sensible defaults for RNA-seq expression data

Source: R/quickmap.R
quickmap.Rd

Generate a heatmap using pheatmap with sensible defaults for RNA-seq.

Usage

quickmap(x, metadata = NULL, remove_var = NULL, ...)

Arguments

x

numeric matrix to be passed onto pheatmap function

metadata

column metadata to add to heatmap annotation. Default NULL

remove_var

Remove this proportion of features based on variance across rows. Default NULL.

...

args to be passed to pheatmap() function

Value

pheatmap object. See ?pheatmap::pheatmap() for details

Details

The default arguments to pheatmap::pheatmap() are:

    • scale = "row"

    • show_rownames = FALSE

    • border_col = NA

    • cluster_rows = TRUE

    • cluster_cols = TRUE

    • color = colorRampPalette(c("dodgerblue3", "grey99", "firebrick3"))(30)

    • treeheight_row = 0

    • clustering_distance_rows = "correlation"

    • clustering_distance_cols = "euclidean"

    • clustering_method = "ward.D2"

    • angle_col = 315

Examples


# Display heatmap of scaled count data and add title to the plot
quickmap(GSE161650_lc, main = "THZ1 vs DMSO")


# Override quickmap defaults by supplying additional args
quickmap(GSE161650_lc, cluster_rows = FALSE, cluster_cols = FALSE)