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In cmmr/rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

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Description

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Arguments

grid	Color palette name, or a list with entries for label, colors, range, bins, na.color, and/or guide. See the Track Definitions section for details. Default: list(label = "Grid Value", colors = "imola")
label	Label the matrix rows and columns. You can supply a list or logical vector of length two to control row labels and column labels separately, for example label = c(rows = TRUE, cols = FALSE), or simply label = c(T, F). Other valid options are "rows", "cols", "both", "bottom", "right", and "none". Default: TRUE
label_size	The font size to use for the row and column labels. You can supply a numeric vector of length two to control row label sizes and column label sizes separately, for example c(rows = 20, cols = 8), or simply c(20, 8). Default: NULL, which computes: pmax(8, pmin(20, 100 / dim(mtx)))
rescale	Rescale rows or columns to all have a common min/max. Options: "none", "rows", or "cols". Default: "none"
trees	Draw a dendrogram for rows (left) and columns (top). You can supply a list or logical vector of length two to control the row tree and column tree separately, for example trees = c(rows = T, cols = F), or simply trees = c(T, F). Other valid options are "rows", "cols", "both", "left", "top", and "none". Default: TRUE
clust	Clustering algorithm for reordering the rows and columns by similarity. You can supply a list or character vector of length two to control the row and column clustering separately, for example clust = c(rows = "complete", cols = NA), or simply clust = c("complete", NA). Options are: FALSE or NA - Disable reordering. An hclust class object E.g. from stats::hclust(). A method name - "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", or "centroid". Default: "complete"
dist	Distance algorithm to use when reordering the rows and columns by similarity. You can supply a list or character vector of length two to control the row and column clustering separately, for example dist = c(rows = "euclidean", cols = "maximum"), or simply dist = c("euclidean", "maximum"). Options are: A dist class object E.g. from stats::dist() or bdiv_distmat(). A method name - "euclidean", "maximum", "manhattan", "canberra", "binary", or "minkowski". Default: "euclidean"
tree_height, track_height	The height of the dendrogram or annotation tracks as a percentage of the overall grid size. Use a numeric vector of length two to assign c(top, left) independently. Default: 10 (10% of the grid's height)
asp	Aspect ratio (height/width) for entire grid. Default: 1 (square)
legend	Where to place the legend. Options are: "right" or "bottom". Default: "right"
title	Plot title. Set to TRUE for a default title, NULL for no title, or any character string. Default: TRUE
...	Additional arguments to pass on to ggplot2::theme().

Value

A ggplot2 plot.
The computed data points and ggplot command are available as ⁠$data⁠ and ⁠$code⁠, respectively.

cmmr/rbiom documentation built on April 28, 2024, 6:38 a.m.