plotWaterfall: Plot waterfall

In acidgenomics/r-acidplots: Acid Genomics Plot Functions and Themes

Plot waterfall

Description

Plot waterfall

Usage

plotWaterfall(object, ...)

## S4 method for signature 'DFrame'
plotWaterfall(
  object,
  sampleCol,
  valueCol,
  interestingGroups = NULL,
  trans = c("identity", "log2", "log10"),
  fill = purpleOrange(1L),
  labels = list(title = NULL, subtitle = NULL)
)

## S4 method for signature 'SummarizedExperiment'
plotWaterfall(
  object,
  assay = 1L,
  fun = c("mean", "sum"),
  interestingGroups = NULL,
  ...
)

## S4 method for signature 'data.frame'
plotWaterfall(
  object,
  sampleCol,
  valueCol,
  interestingGroups = NULL,
  trans = c("identity", "log2", "log10"),
  fill = purpleOrange(1L),
  labels = list(title = NULL, subtitle = NULL)
)

Arguments

object	Object.
sampleCol	character(1). Column name of discrete samples to plot on X axis.
valueCol	character(1). Column name of continues values to plot on Y axis.
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.
trans	character(1). Name of the axis scale transformation to apply. For more information: help(topic = "scale_x_continuous", package = "ggplot2")
fill	character(1). R color name or hex color code (e.g. "#AF52DE").
labels	list. ggplot2 labels. See ggplot2::labs() for details.
assay	vector(1). Assay name or index position.
fun	function.
...	Additional arguments.

Value

ggplot.

Note

Updated 2023-08-10.

See Also

• Ordering bars from lowest to highest value in each facet

• Ordering bars within facets using tidytext

Examples

data(RangedSummarizedExperiment, package = "AcidTest")

## data.frame ====
object <- data.frame(
    "cellId" = AcidGenerics::autopadZeros(
        object = paste("cell", seq_len(12L), sep = "_")
    ),
    "ic50" = seq(
        from = 0.1,
        to = 10L,
        length.out = 12L
    ),
    "tumorType" = rep(
        x = c("breast", "bladder"),
        times = 6L
    ),
    "tumorSubtype" = rep(
        x = c("benign", "malignant"),
        each = 6L
    )
)
plotWaterfall(
    object = object,
    sampleCol = "cellId",
    valueCol = "ic50",
    interestingGroups = c("tumorType", "tumorSubtype"),
    trans = "log10"
)

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
plotWaterfall(object, trans = "identity")

acidgenomics/r-acidplots documentation built on March 30, 2024, 10:16 p.m.