aoMatrix: plot an ordered (sorted) matrix

In nickytong/GenAnalysis: Genomic Analysis

Description

this is an enhancement of aMatrix where one can specify Rowv and Colv as in heatmap.2 typical application is that one can need to order according to a phenotype, i.e. EMT score

Usage

aoMatrix(mat, color = bluered(50), display_numbers = TRUE, scale = "none",
  Rowv = NULL, Colv = NULL, clustering_distance_rows,
  clustering_distance_cols, clustering_method = "ward.D2", return = FALSE,
  annotation = NA, annotation_colors = NA, labRow = NA, labCol = NA,
  ...)

Arguments

mat	a matrix to be plotted
color	color pallete ( a vector of colors)
display_numbers	whether to display numbers
scale	ways to scale the values
Rowv	either NULL or a vector of integers for row ordering
Colv	either NULL or a vector of integers for column ordering
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.
clustering_method	clustering method used. Accepts the same values as hclust.
return	whether to return a list of orders
annotation	data frame that specifies the annotations shown on top of the columns. Each row defines the features for a specific column. The columns in the data and rows in the annotation are matched using corresponding row and column names. Note that color schemes takes into account if variable is continuous or discrete.
...	additional parameters to be passed to aheatmap (pheatmap)

Details

The working horce is aMatrix (more precisely its code). We only need to computer row order and column order and pass the reordered matrix to aMatrix. Ordering is determined first by looking at Rowv and Colv. If either one is not specified, order is computed based on clustering with a given distance and linkage rule. If even clustering is not specified, then there is no ordering.

nickytong/GenAnalysis documentation built on July 20, 2019, 8:57 a.m.