hagenheat: hagenheat

In grasshoppermouse/hagenutils: Plots, tables, and inlines for knitr

hagenheat

Description

Basic heatmap using ggplot, dist, and seriation. No dendrograms are plotted.

Usage

hagenheat(
  d,
  method = "seriate",
  seriation_method = NULL,
  independent = F,
  hc_method = "ward.D",
  dist_method = "euclidean",
  scale. = "none",
  viridis_option = "D",
  wrap_labels = T,
  rotate_labels = F,
  ann_col = NULL,
  rev_col = F,
  rev_row = F
)

Arguments

d	A data frame, matrix, or dist object. Column 1 of a data frame can be row labels. Remaining columns must be numeric.
method	"seriate" or "hclust". Default: "seriate"
seriation_method	If not specified, 'Spectral' will be used for dist objects, and 'PCA' for matrices and data frames.
independent	Whether to seriate a matrix using matrix methods (F) or separate distance matrices for rows and columns (T). Default: F
hc_method	Agglomeration method from hclust, Default: 'ward.D'
scale.	Whether to scale rows ('row'), columns ('column'), or neither ('none'), Default: 'none'
viridis_option	One of the viridis color options, 'A', 'B', 'C', 'D', 'E', Default: 'D'
wrap_labels	Logical. Wrap the x-axis labels. Default: T
rotate_labels	Logical. Rotate the x-axis labels by 90 degrees. Default: F
ann_col	A data frame with two variables. The first column must be the names of the columns of 'd'. The second column contains the annotation values.
rev_col	Reverse column order. Default: F
rev_row	Reverse row order. Default: F
dist	Distance method from dist, Default: 'euclidean'

Details

Produces a very simple ggplot heatmap using viridis colors. Rows and columns are ordered using the seriation package. For data frames, first column must be row labels. Remaining columns must be numeric. Scaling, if performed, occurs after seriation, and is therefore only for display purposes. Seriation methods for objects when independent=T: list_seriation_methods('dist'). Seriation methods for matrices and data frames when independent=F: list_seriation_methods('matrix').

Value

A ggplot object

See Also

seriate seriation_methods new_scale_fill

Examples

## Not run: 
if(interactive()){
 hagenheat(mtcars, scale. = 'column')
 }

## End(Not run)

grasshoppermouse/hagenutils documentation built on Dec. 6, 2024, 8:31 p.m.