Get a plot

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).

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

if (FALSE) { # \dontrun{
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
)
} # }