arrowPlot {Harman} | R Documentation

## PCA before and after arrow plot for harman results

### Description

Generates an arrow plot for an instance of `harmanresults`. The tail of the arrow is the starting point (original) in principle coordinates, while the arrow head is the new point (corrected) in principle coordinates. It can be observed that on principle components that have undergone correction (codeharmanresults$stats$correction < 1.0), the samples within a batch will be coordinately moved towards `0` on that priciple component.

### Usage

    arrowPlot(harmanresults, pc_x = 1, pc_y = 2, colBy = "batch",
      palette = "rainbow", col, length = 0.1, legend = TRUE, ...)

### Arguments

`harmanresults` | an instance of `harmanresults`.
`pc_x` | integer, principle component for the plot x dimension.
`pc_y` | integer, principle component for the plot y dimension.
`colBy` | string, colour the points by the experimental or batch variable; legal values are `expt` and `batch`. The palette function specified in `palette` is used. This parameter is overridden by `col`.
`palette` | string, the function to call to create a vector of contiguous colours with the levels of factor in `colBy` steps.
`col,` | colour vector for the points. This parameter overrides `palette`.
`length` | length of the `arrow` heads, default is 0.1.
`legend` | logical, whether to display a legend on the plot
`...` | further arguments passed to or from other methods.

### Details

Generates a Principle Component plot for an instance of `harmanresults`. If a vector of colours is supplied via the `col` argument, then a legend will not be drawn.

### Value

None

### See Also

`harmanresults` `plot.harmanresults`

### Examples

    library(HarmanData)
    data(OLF)
    expt <- olf.info$Treatment
    batch <- olf.info$Batch
    olf.harman <- harman(olf.data, expt, batch)
    arrowPlot(olf.harman, pc_x=2, pc_y=3, length=0.2)

[Package Harman version 1.12.0 Index]