Bar plot of clonal diversity metrics

The plot_diversity() plots the requested clonal diversity metric

This function can plot a variety of clonal diversity metrics for a dataset (richness, Simpson diversity index, Shannon-Wiener index, etc.). See get_all_div_metrics() for all available options. By default it return a barplot with one bar for each sample in the dataset. If a grouping column (of the metadata) is supplied, then samples will be grouped and bar heights will reflect the average diversity metric across the group, with error bars showing the standard deviation.

Usage

plot_diversity(
  div,
  metric = get_all_div_metrics(),
  q = 2,
  percent = 90,
  group_col = NULL,
  label_col = "Sample",
  flip = FALSE,
  facet = FALSE,
  log_scale = FALSE,
  samples = NULL,
  return_data = FALSE,
  color_scheme = NULL,
  x_var = NULL
)

Arguments

div: a list created by the calculate_diversity() function with diversity metrics for each sample
metric: the diversity metric to use (e.g. shannon, simpson, etc.)
q: (optional) for 'renyi' and 'hill' metrics, the order q of the diversity index
percent: (optional) for 'dXX' metric, the percentage 'XX' between 0 and 100
group_col: (optional) if supplied, a column of the metadata that will be used to group samples
label_col: (optional) labels for the samples
flip: (optional) if TRUE, flip the x and y-axes (default is FALSE)
facet: (optional) if TRUE, plot with separate facets, or sub-plots for each group (default is FALSE)
log_scale: (optional) if TRUE, use log-scale for the y-axis (default is FALSE)
samples: (optional) the samples to include in the plot (default is all samples)
return_data: (optional) if TRUE, return the data used to make the plot (default is FALSE)
color_scheme: (optional) a color scheme for the plot
x_var: (optional) the variable to show on the x-axis, if other than "sample_id"

Value

A list with two objects:

$plot - a ggplot object with the plot of the requested diversity metric

$data - if return_data is TRUE, the data frame used to make the plot

Examples

folder = system.file("extdata/SJTRC_TIRTL_seq_longitudinal",
  package = "TIRTLtools")
sjtrc = load_tirtlseq(folder,
  meta_columns = c("marker", "timepoint", "version"), sep = "_",
  verbose = FALSE)

div = calculate_diversity(sjtrc, chain = "beta", metrics = "d50")
#> 
#> -- Calculating diversity indices for sample 1 of 6.
#> -- Calculating diversity indices for sample 2 of 6.
#> -- Calculating diversity indices for sample 3 of 6.
#> -- Calculating diversity indices for sample 4 of 6.
#> -- Calculating diversity indices for sample 5 of 6.
#> -- Calculating diversity indices for sample 6 of 6.
plot_diversity(div, metric = "d50")

Usage

Arguments

Value

See also

Examples