PlotFileScatters {FlowSOM} | R Documentation

## PlotFileScatters

### Description

Make a scatter plot per channel for all provided files

### Usage

    PlotFileScatters(
      input,
      channels = NULL,
      yMargin = NULL,
      yLabel = c("marker"),
      quantiles = NULL,
      names = NULL,
      groups = NULL,
      color = NULL,
      legend = FALSE,
      maxPoints = 50000,
      ncol = NULL,
      nrow = NULL,
      silent = FALSE,
      plotFile = "FileScatters.png"
    )

### Arguments

`input` | Either a flowSet, a flowFrame (output from the `AggregateFlowFrames` function) or a vector of paths pointing to fcs files
`channels` | Vector of channels or markers that need to be plotted, if NULL (default), all channels from the input will be plotted
`yMargin` | Optional parameter to specify the margins of the y-axis
`yLabel` | Determines the label of the y-axis. Can be "marker" and\or "channel". Default = "marker".
`quantiles` | If provided (default NULL), a numeric vector with values between 0 and 1. These quantiles are indicated on the plot
`names` | Optional parameter to provide filenames. If `NULL` (default), the filenames will be numbers. Duplicated filenames will be made unique.
`groups` | Optional parameter to specify groups of files, should have the same length as the `input`. Id `NULL` (default), all files will be plotted in the same color
`color` | Optional parameter to provide colors. Should have the same lengths as the number of groups (or 1 if `groups` is `NULL`)
`legend` | Logical parameter to specify whether the group levels should be displayed. Default is `FALSE`
`maxPoints` | Total number of data points that will be plotted per channel, default is 50000
`ncol` | Number of columns in the final plot, optional
`nrow` | Number of rows in the final plot, optional
`silent` | If FALSE, prints an update every time it starts processing a new file. Default = FALSE.
`plotFile` | Path to png file, default is "FileScatters.png". If `NULL`, the output will be a list of ggplots

### Value

List of ggplot objects if `plot` is `FALSE`, otherwise `filePlot` with plot is created.

### Examples

    # Preprocessing
    fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
    ff <- flowCore::read.FCS(fileName)
    ff <- flowCore::compensate(ff, flowCore::keyword(ff)[["SPILL"]])
    ff <- flowCore::transform(ff,
             flowCore::transformList(colnames(flowCore::keyword(ff)[["SPILL"]]),
                                    flowCore::logicleTransform()))

    flowCore::write.FCS(ff[1:1000, ], file = "ff_tmp1.fcs")
    flowCore::write.FCS(ff[1001:2000, ], file = "ff_tmp2.fcs")
    flowCore::write.FCS(ff[2001:3000, ], file = "ff_tmp3.fcs")

    # Make plot
    PlotFileScatters(input = c("ff_tmp1.fcs", "ff_tmp2.fcs", "ff_tmp3.fcs"),
                     channels = c("Pacific Blue-A",
                                  "Alexa Fluor 700-A",
                                  "PE-Cy7-A"),
                     maxPoints = 1000)

[Package FlowSOM version 2.2.0 Index]