plotCorrelation: Correlation X-Y scatterplot

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

Correlation X-Y scatterplot

Description

Correlation X-Y scatterplot

Usage

plotCorrelation(object, ...)

## S4 method for signature 'DFrame'
plotCorrelation(
  object,
  xCol,
  yCol,
  pointLabelCol = NULL,
  labels = list(title = NULL, subtitle = NULL, x = NULL, y = NULL),
  trans = c("identity", "log10", "log2"),
  r2 = TRUE,
  se = TRUE,
  colors = list(dots = "black", line = "black", se = "gray")
)

## S4 method for signature 'Matrix'
plotCorrelation(object, xCol, yCol, labelPoints = FALSE, ...)

## S4 method for signature 'SummarizedExperiment'
plotCorrelation(object, assay = 1L, ...)

## S4 method for signature 'data.frame'
plotCorrelation(
  object,
  xCol,
  yCol,
  pointLabelCol = NULL,
  labels = list(title = NULL, subtitle = NULL, x = NULL, y = NULL),
  trans = c("identity", "log10", "log2"),
  r2 = TRUE,
  se = TRUE,
  colors = list(dots = "black", line = "black", se = "gray")
)

## S4 method for signature 'matrix'
plotCorrelation(object, xCol, yCol, labelPoints = FALSE, ...)

Arguments

object	Object.
xCol, yCol	character(1) or integer(1). X and Y column name or position.
pointLabelCol	character(1) or NULL. For data.frame method, which column name or position should be used to label points on the plot?
labels	list. ggplot2 labels. See ggplot2::labs() for details.
trans	character(1). Name of the axis scale transformation to apply. For more information: help(topic = "scale_x_continuous", package = "ggplot2")
r2	logical(1). Show information on the lm fit? This includes the equation, and the coefficient of determination (R^2). Refer to ggpmisc::stat_poly_eq for details.
se	logical(1). Display confidence interval around the lm fit line? Refer to ggplot2::geom_smooth for details.
colors	list(3). Named list defining the colors of dots, line, and se, for confidence interval standard error.
labelPoints	logical(1). For matrix method, label points on plot with row names?
...	Additional arguments.
assay	vector(1). Assay name or index position.

Value

Plot.

Correlation coefficient calculations

Correlation coefficient calcluations are generated by ggpmisc::stat_poly_eq. Refer to the ggpmisc GitHub repo for details.

Note

Updated 2023-12-10.

See Also

• ggpmisc::stat_poly_eq.

• ggplot2::geom_smooth.

Examples

data(RangedSummarizedExperiment, package = "AcidTest")

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
plotCorrelation(
    object = object,
    xCol = 1L,
    yCol = 2L,
    trans = "identity"
)

acidgenomics/minimalism documentation built on April 1, 2024, 10:34 a.m.