metacoder (version 0.3.7)

heat_tree_matrix: Plot a matrix of heat trees

Description

Plot a matrix of heat trees for showing pairwise comparisons. A larger, labelled tree serves as a key for the matrix of smaller unlabelled trees. The data for this function is typically created with compare_groups,

Usage

heat_tree_matrix(
  obj,
  data,
  label_small_trees = FALSE,
  key_size = 0.6,
  seed = 1,
  output_file = NULL,
  row_label_color = diverging_palette()[3],
  col_label_color = diverging_palette()[1],
  row_label_size = 12,
  col_label_size = 12,
  ...,
  dataset = NULL
)

Arguments

obj

A taxmap object

data

The name of a table in obj$data that is the output of compare_groups or in the same format.

label_small_trees

If TRUE add labels to small trees as well as the key tree. Otherwise, only the key tree will be labeled.

key_size

The size of the key tree relative to the whole graph. For example, 0.5 means half the width/height of the graph.

seed

That random seed used to make the graphs.

output_file

The path to one or more files to save the plot in using ggsave. The type of the file will be determined by the extension given. Default: Do not save plot.

row_label_color

The color of the row labels on the right side of the matrix. Default: based on the node_color_range.

col_label_color

The color of the columns labels along the top of the matrix. Default: based on the node_color_range.

row_label_size

The size of the row labels on the right side of the matrix. Default: 12.

col_label_size

The size of the columns labels along the top of the matrix. Default: 12.

...

Passed to heat_tree. Some options will be overwritten.

dataset

DEPRECIATED. use "data" instead.

Examples

if (FALSE) {
# Parse dataset for plotting
x <- parse_tax_data(hmp_otus, class_cols = "lineage", class_sep = ";",
                    class_key = c(tax_rank = "taxon_rank", tax_name = "taxon_name"),
                    class_regex = "^(.+)__(.+)$")

# Convert counts to proportions
x$data$otu_table <- calc_obs_props(x, data = "tax_data", cols = hmp_samples$sample_id)

# Get per-taxon counts
x$data$tax_table <- calc_taxon_abund(x, data = "otu_table", cols = hmp_samples$sample_id)

# Calculate difference between treatments
x$data$diff_table <- compare_groups(x, data = "tax_table",
                                    cols = hmp_samples$sample_id,
                                    groups = hmp_samples$body_site)

# Plot results (might take a few minutes)
heat_tree_matrix(x,
                 data = "diff_table",
                 node_size = n_obs,
                 node_label = taxon_names,
                 node_color = log2_median_ratio,
                 node_color_range = diverging_palette(),
                 node_color_trans = "linear",
                 node_color_interval = c(-3, 3),
                 edge_color_interval = c(-3, 3),
                 node_size_axis_label = "Number of OTUs",
                 node_color_axis_label = "Log2 ratio median proportions")

}