plotScatter {sights} | R Documentation

## Scatter plot

### Description

Construct a scatter plot of all pairwise combinations of replicates

### Usage

    plotScatter(plotMatrix, repIndex, plotRows = NULL, plotCols = NULL,
      plotName = NULL, ...)

### Arguments

`plotMatrix` | Data frame or numeric matrix. Columns are plates, and rows are plate wells.
`repIndex` | Optional. Vector of labels indicating replicate group. Each index in the vector matches the corresponding column of plotMatrix. If NULL then all plates are plotted together without grouping.
`plotRows, plotCols` | Optional integer vector. Indicate which row/column numbers from the plotMatrix should be plotted. If NULL then all rows/columns from the plotMatrix are used.
`plotName` | Optional. Name of plotMatrix for plot title.
`...` | Optional. Additional parameters passed to `geom_point`.

### Details

Scatter plots with robust regression lines of replicate plates can reveal a kind of bias which acts independently of within-plate biases and which cannot be detected by heat maps (`plotHeatmap`) or auto-correlation plots (`plotAutoco`). A mixture of active and inactive features should produce a zero-correlation flat regression line within most of the range and a positively sloped line within the active range(s) at the extreme(s) of the distribution.

### Value

List of modifiable ggplot2 objects

### See Also

Other graphical devices: `plot3d`, `plotAutoco`, `plotBox`, `plotHeatmap`, `plotHist`, `plotIGFit`

### Examples

    ## load dataset
    data(ex_dataMatrix)

    ## plot raw data
    plotScatter(plotMatrix = ex_dataMatrix, repIndex = c(1,1,1), plotCols = 5:7,
    plotName = 'Example')
    ## normalize data matrix using any method and store in new variable
    ex_normMatrix <- normZ(dataMatrix = ex_dataMatrix, dataCols = 5:10)
    ## plot normalized data
    plotScatter(plotMatrix = ex_normMatrix, repIndex = c(1,1,1), plotCols = 1:3,
    plotName = 'Example')

[Package sights version 1.10.0 Index]