plot_matrix_heatmap: Plot a clustered heatmap

Description Usage Arguments Value Examples

View source: R/plot_matrix_heatmap.R

Description

Draws a clustered heatmap using clustering methods implemented in the popular R package pheatmap. Returns a ggplot2 object

Usage

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plot_matrix_heatmap(matrix, scale = "row", limits = NULL,
  color_scale_type = "diverge", color_scale = c("blue", "lightyellow",
  "red"), scale_midpoint = 0, cluster_rows = T, cluster_cols = T,
  clustering_distance_rows = "euclidean",
  clustering_method_rows = "complete",
  clustering_distance_cols = "euclidean",
  clustering_method_cols = "complete", square_tiles = F)

Arguments

matrix

a matrix of values

scale

"rows" or "cols" or "none"; indicates whether values should be centered and scaled in the row direction or the column direction or none.

limits

minimum and maximum values to define the range of the color scale

color_scale_type

"diverge", "seq" or "rescale".

color_scale

vector of colors to use for color scale; different options for color_scale_type requires different number of colors - "diverge" (3 colors), "seq" (2 colors), "rescale" (3 colors)

scale_midpoint

numeric; value of midpoint for "diverge" and "rescale" color scales

cluster_rows

logical; if rows should be clustered

cluster_cols

logical; if columns should be clustered

clustering_distance_rows

distance measure used in clustering rows. Possible values are "correlation", "euclidean", "maximum", "manhattan", "canberra", "binary", or "minkowski" (defined in dist() function.)

clustering_method_rows

clustering method used for rows. Accepts the same values as hclust: "ward.D", "ward.D2", "single", "complete", "average" (=UPGMA), "mcquitty" (=WPGMA), "median" (=WPGMC) or "centroid" (=UPGMC).

clustering_distance_cols

distance measure used in clustering columns. Possible values are the same as clustering_distance_rows.

clustering_method_cols

clustering method used for columns. Accepts the same values as clustering_method_rows.

square_tiles

logical; if tiles should be made square

Value

a ggplot2 object

Examples

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jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.