taxa_heatmap: Display taxa abundances as a heatmap.

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

Display taxa abundances as a heatmap.

Description

Display taxa abundances as a heatmap.

Usage

taxa_heatmap(
  biom,
  rank = -1,
  taxa = 6,
  grid = "bilbao",
  color.by = NULL,
  order.by = NULL,
  other = FALSE,
  unc = "singly",
  lineage = FALSE,
  label = TRUE,
  label_size = NULL,
  rescale = "none",
  trees = TRUE,
  clust = "complete",
  dist = "euclidean",
  asp = 1,
  tree_height = 10,
  track_height = 10,
  legend = "right",
  title = NULL,
  xlab.angle = "auto",
  ...
)

Arguments

biom	An rbiom object, such as from as_rbiom(). Any value accepted by as_rbiom() can also be given here.
rank	What rank(s) of taxa to display. E.g. "Phylum", "Genus", ".otu", etc. An integer vector can also be given, where 1 is the highest rank, 2 is the second highest, -1 is the lowest rank, -2 is the second lowest, and 0 is the OTU "rank". Run biom$ranks to see all options for a given rbiom object. Default: -1.
taxa	Which taxa to display. An integer value will show the top n most abundant taxa. A value 0 <= n < 1 will show any taxa with that mean abundance or greater (e.g. 0.1 implies >= 10%). A character vector of taxa names will show only those named taxa. Default: 6.
grid	Color palette name, or a list as expected plot_heatmap(). Default: "bilbao"
color.by	A character vector of metadata fields to display as tracks at the top of the plot. Or, a list as expected by the tracks argument of plot_heatmap(). Default: NULL
other	Sum all non-itemized taxa into an "Other" taxa. When FALSE, only returns taxa matched by the taxa argument. Specifying TRUE adds "Other" to the returned set. A string can also be given to imply TRUE, but with that value as the name to use instead of "Other". Default: FALSE
unc	How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are: "singly" - Replaces them with the OTU name. "grouped" - Replaces them with a higher rank's name. "drop" - Excludes them from the result. "asis" - To not check/modify any taxa names. Default: "singly" Abbreviations are allowed.
lineage	Include all ranks in the name of the taxa. For instance, setting to TRUE will produce ⁠Bacteria; Actinobacteria; Coriobacteriia; Coriobacteriales⁠. Otherwise the taxa name will simply be Coriobacteriales. You want to set this to TRUE when unc = "asis" and you have taxa names (such as Incertae_Sedis) that map to multiple higher level ranks. Default: FALSE
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"
asp	Aspect ratio (height/width) for entire grid. Default: 1 (square)
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)
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
xlab.angle	Angle of the labels at the bottom of the plot. Options are "auto", '0', '30', and '90'. Default: "auto".
...	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.

See Also

Other taxa_abundance: taxa_boxplot(), taxa_corrplot(), taxa_stacked(), taxa_stats(), taxa_sums(), taxa_table()

Other visualization: adiv_boxplot(), adiv_corrplot(), bdiv_boxplot(), bdiv_corrplot(), bdiv_heatmap(), bdiv_ord_plot(), plot_heatmap(), rare_corrplot(), rare_multiplot(), rare_stacked(), stats_boxplot(), stats_corrplot(), taxa_boxplot(), taxa_corrplot(), taxa_stacked()

Examples

    library(rbiom)
    
    # Keep and rarefy the 10 most deeply sequenced samples.
    hmp10 <- rarefy(hmp50, n = 10)
    
    taxa_heatmap(hmp10, rank = "Phylum", color.by = "Body Site")
    
    taxa_heatmap(hmp10, rank = "Genus", color.by = c("Sex", "Body Site"))
    
    taxa_heatmap(hmp10, rank = "Phylum", color.by = list(
      'Sex'       = list(colors = c(Male = "#0000FF", Female = "violetred")), 
      'Body Site' = list(colors = "muted", label = "Source") ))
    

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