getPlot: Get a plot

In primitybio/cellengine-r-toolkit: 'CellEngine' API Toolkit

Get a plot

Description

Gets a plot for an FcsFile. If in RStudio or Jupyter and display is TRUE (default), displays the image. If destination is provided, also saves the image as a PNG file. In all cases, returns the PNG-encoded bytes (invisibly, if display is TRUE).

Usage

getPlot(
  experimentId,
  fcsFileId,
  plotType,
  xChannel,
  yChannel = "",
  zChannel = "",
  params = list(),
  destination = NULL,
  overwrite = FALSE,
  display = TRUE
)

Arguments

experimentId	character ID of experiment.
fcsFileId	character ID of FcsFile
plotType	character Plot type, one of: "contour", "dot", "density", or "histogram"
xChannel	character X channel name
yChannel	character Y channel name
zChannel	character Z channel name
params	list Optional query parameters: axesQ logical Display axes lines. Defaults to TRUE. axisLabelsQ logical Display axis labels. Defaults to TRUE. color character Case-insensitive string in the format #rgb, #rgba, #rrggbb or #rrggbbaa. The foreground color, i.e. color of curves in "histogram" and "contour" plots, dots in "dot" plots. compensation character ID of compensation to use for gating and display, or one of UNCOMPENSATED or FILE_INTERNAL. gateLabel character One of "eventcount", "mean", "median", "percent", "mad", "cv", "stddev", "geometricmean", "name", "none". gateLabelFontSize double Font size for gate labels. height double Image height. Defaults to 228. percentileStart double For contour plots, the percentile of the first contour. percentileStep double For contour plots, the percentile step between each contour. populationId character Population ID. Defaults to ungated. postSubsampleN double Randomly subsample the file to contain this many events after gating. postSubsampleP double Randomly subsample the file to contain this percent of events (0 to 1) after gating. renderGates logical Render gates into the image. seed double Seed for random number generator used for subsampling. Use for deterministic reproducible subsampling. If omitted, a pseudo-random value is used. smoothing double For density and contour plots, adjusts the amount of smoothing. Defaults to 0 (no smoothing). Set to 1 for typical smoothing. Higher values (up to 10) increase smoothing. strokeThickness double The thickness of histogram and contour plot lines. Defaults to 1. tickLabelsQ logical Display tick labels. Defaults to FALSE. ticksQ logical Display ticks. Defaults to TRUE. width Integer Image width. Defaults to 228. xAxisLabelQ logical Display x axis label. Overrides axisLabelsQ. xAxisQ logical Display x axis line. Overrides axesQ. xTickLabelsQ logical Display x tick labels. Overrides tickLabelsQ. xTicksQ logical Display x ticks. Overrides ticksQ. yAxisLabel logical Display y axis label. Overrides axisLabelsQ. yAxisQ logical Display y axis line. Overrides axesQ. yTickLabelsQ logical Display y tick labels. Overrides tickLabelsQ. yTicksQ logical Display y ticks. Overrides ticksQ.
destination	character If specified, write the image to file.
overwrite	logical If a destination is specified, allows destination file to be overwritten.
display	logical Display the image. Defaults to TRUE.

Examples

## Not run: 
parameters <- list(
  "width" = 400,
  "height" = 400,
  "axesQ" = FALSE,
  "ticksQ" = FALSE,
  "color" = "#ff0000",
  "renderGates" = TRUE,
  "smoothing" = 0.75,
)
getPlot(experimentId,
  fcsFileId,
  plotType = "dot",
  xChannel = "FSC-A",
  yChannel = "FSC-W",
  params = parameters
)

## End(Not run)

primitybio/cellengine-r-toolkit documentation built on Oct. 19, 2024, 1:17 a.m.