pheatmap1: wrapper around pheatmap

In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

wrapper around pheatmap

Description

wrapper around pheatmap

Usage

pheatmap1(
  pmat,
  annotation = NULL,
  annotation_colors = NULL,
  annotation_col = NULL,
  annotation_row = NULL,
  id_column = TRUE,
  border_color = NA,
  clustering_callback = function(hc, ...) {     dendsort::dendsort(hc) },
  clustering_distance_rows = "euclidean",
  clustering_distance_cols = "euclidean",
  min_vals_row = 1,
  min_vals_col = 1,
  na_col = "gray",
  ...
)

Arguments

pmat	data frame to plot as matrix. can have an additional id column (if id_column == TRUE)
annotation	data frame with 'samp' field, and additional annotations
annotation_colors	tidy data frame with 3 fields: 'type' - name of the annotation, e.g. 'tissue', and pairs of 'variable' and 'color', e.g. variable='tumor', color='green'
annotation_col	character vector with column names from 'annotation' to use to annotate columns
annotation_row	character vector with column names from 'annotation' to use to annotate rows
id_column	TRUE if pmat's first column contains row ids
border_color	color of cell borders on heatmap, use NA if no border should be drawn.
clustering_callback	callback function to modify the clustering. Is called with two parameters: original hclust object and the matrix used for clustering. Must return a hclust object.
clustering_distance_rows	distance measure used in clustering rows. Possible values are "correlation" for Pearson correlation and all the distances supported by dist, such as "euclidean", etc. If the value is none of the above it is assumed that a distance matrix is provided.
clustering_distance_cols	distance measure used in clustering columns. Possible values the same as for clustering_distance_rows.
na_col	specify the color of the NA cell in the matrix.
...	graphical parameters for the text used in plot. Parameters passed to grid.text, see gpar.

tanaylab/gpatterns documentation built on May 15, 2023, 6:23 p.m.