Plot waterfall

Plot waterfall

Usage

plotWaterfall(object, ...)

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

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

# S4 method for class '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")