PlotFileScatters: PlotFileScatters

In saeyslab/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

PlotFileScatters

Description

Make a scatter plot per channel for all provided files

Usage

PlotFileScatters(
  input,
  fileID = "File",
  channels = NULL,
  yLim = NULL,
  yLabel = "marker",
  quantiles = NULL,
  names = NULL,
  groups = NULL,
  color = NULL,
  legend = FALSE,
  maxPoints = 50000,
  ncol = NULL,
  nrow = NULL,
  width = NULL,
  height = NULL,
  silent = FALSE,
  plotFile = "FileScatters.png",
  ...
)

Arguments

input	Either a flowSet, a flowFrame with a file ID column (e.g. output from the AggregateFlowFrames includes a "File" column) or a vector of paths pointing to FCS files
fileID	Name of the file ID column when the input is a flowFrame, default to "File" (File ID column in the AggregateFlowFrames flowFrame output).
channels	Vector of channels or markers that need to be plotted, if NULL (default), all channels from the input will be plotted
yLim	Optional vector of a lower and upper limit of the y-axis
yLabel	Determines the label of the y-axis. Can be "marker" and\or "channel" or abbrevations. 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
width	Width of png file. By default NULL the width parameter is estimated based on the input.
height	Height of png file. By default NULL the width parameter is estimated based on the input.
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
...	Arguments for read.FCS (e.g. truncate_max_range)

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)

saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.