plotOrderedBubble

Generate ordered proportional bubbleplots from raw count object with barcodes labelled above a specified threshold

Usage

plotOrderedBubble(
  dgeObject,
  title = "Proportional Bubble Plot",
  orderSample = NULL,
  group = NULL,
  displaySamples = NULL,
  displayBarcodes = NULL,
  proportionCutoff = 10,
  colorDominant = FALSE,
  filterCutoff = NULL,
  labelBarcodes = TRUE,
  legend = TRUE,
  pseudoCount = FALSE
)

Arguments

dgeObject

DGEList object with barcode counts.

title

Plot title (string). Default = `Proportional Bubble Plot`.

orderSample

Name of sample to order by (string).

group

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

displaySamples

Optional, vector of samples to display - keep the order of vector.

displayBarcodes

Optional, vector of barcodes to display.

proportionCutoff

barcodes represented at a percentage within any sample above this threshold will be labelled (decimal). Default = `10`.

colorDominant

Only color clones with frequency above `proportionCutoff` and others grey (boolean). Default = `FALSE`.

filterCutoff

Barcodes below this threshold in `orderSample` will be filtered in all samples (boolean). Default = `TRUE`.

labelBarcodes

Label barcodes with a proportion larger than proportionCutoff in any sample (boolean). Default = `TRUE`.

legend

Show a legend of bubble sizes (boolean). Default = `TRUE`.

pseudoCount

Whether to add a pseudo count of 1 to all counts to display barcodes absent in T0 (boolean). Requires counts to be normalized. Default = `FALSE`.

Value

Returns a bubbleplot of barcodes represented by proportion of total pool

Examples

data(test.dge)
plotOrderedBubble(test.dge, orderSample = "T0-1", filterCutoff = 0.001, group = "Treatment")
#> Warning: Vectorized input to `element_text()` is not officially supported.
#> ℹ Results may be unexpected or may change in future versions of ggplot2.