plot_matrix_heatmap: Plot a clustered heatmap
In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description Usage Arguments Value Examples

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

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)

`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