Plot diversity indices across barcode samples

Plots a dataframe of diversity indices per sample

Usage

plotDivIndexes(
  dgeObject,
  div = NULL,
  metric = "shannon",
  type = "bar",
  group = NULL
)

Arguments

dgeObject

DGEList object with barcode counts.

div

Optional, precomputed diversity metrics calculated by `calcDivIndexes()`.

metric

Diversity metric to plot (string). One of "shannon", "simpson", "invsimpson" or "gini". Default = `shannon`.

type

Plot as bar, point or box plot (string). Default = `bar`.

group

Optional, column name in sample metadata to group samples by (string).

Value

Returns a plot of calculated diversity index per sample

Details

plotDivIndexes

Plots common diversity indices per sample

Examples

data(test.dge)
plotDivIndexes(test.dge, group="Treatment", type="box")