Correlation X-Y scatterplot

## Usage

```
plotCorrelation(object, ...)
# S4 method for DFrame
plotCorrelation(object, labelCol = NULL, ...)
# S4 method for Matrix
plotCorrelation(
object,
xCol,
yCol,
label = FALSE,
labels = NULL,
trans = c("log10", "log2", "identity"),
r2 = TRUE,
se = TRUE,
colors = list(dots = "black", line = "black", se = "gray")
)
# S4 method for SummarizedExperiment
plotCorrelation(object, assay = 1L, ...)
# S4 method for data.frame
plotCorrelation(object, labelCol = NULL, ...)
# S4 method for matrix
plotCorrelation(
object,
xCol,
yCol,
label = FALSE,
labels = NULL,
trans = c("log10", "log2", "identity"),
r2 = TRUE,
se = TRUE,
colors = list(dots = "black", line = "black", se = "gray")
)
```

## Arguments

- object
Object.

- labelCol
`character(1)`

or NULL. For`data.frame`

method, which column should be used to label points on the plot?- ...
Additional arguments.

- xCol, yCol
`character(1)`

or`integer(1)`

. X and Y column name or position.- label
`logical(1)`

. Superimpose sample text labels 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:

- 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.- assay
`vector(1)`

. Assay name or index position.

## Correlation coefficient calculations

Correlation coefficient calcluations are generated by
`ggpmisc::stat_poly_eq()`

. Refer to the ggpmisc GitHub repo for details.

## Examples

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