color_biplot_by_channels: Colors points of a biplot (2d-tSNE, 2d-PCA...) by the...

In ebecht/ebmisc: Misc tools from and for Etienne Becht

Colors points of a biplot (2d-tSNE, 2d-PCA...) by the intensity of channels for each flowframe in the flowset

Description

Colors points of a biplot (2d-tSNE, 2d-PCA...) by the intensity of channels for each flowframe in the flowset

Usage

color_biplot_by_channels(
  matrix,
  x_axis,
  y_axis,
  global_across_channels = T,
  palette = c("blue", "green", "red"),
  resolution = 72,
  data_transformation_reverse = identity,
  file_name = "biplot.pdf",
  raster.height = 480,
  raster.width = 480,
  ...
)

Arguments

matrix	A matrix
x_axis	The column name of the x_axis. Usually the same name you used previously in fs.append
y_axis	The column name of the y_axis. Usually the same name you used previously in fs.append
global_across_channels	Boolean specificying whether the color key should be calibrated across all channels or individually per channel.
palette	A vector of colors that'll be passed to colorRampPalette
resolution	The resolution of the files that'll be imported in the pdf. Default is 72, increase for higher resolution
data_transformation_reverse	The colors will be linearly scaled across the range of the data. If the data was transformed, you may however want the labels which appear in your color-keys to reflect the raw intensities. In this case, this should be the inverse of the function you used to transform your data
file_name	String of the location of the output file (should end in .pdf)
raster.height	height of each embedded raster. Defaults to 480
raster.width	Width of each embedded raster. Defaults to 480
...	passed to plot (suggested: pch=16, cex=0.5 or less)

Note

Since pdf files are vectorized, they can get really big if a lot of data point are plotted. This function thus used bitmap images that are stored in a temporary directory (tmpDir()) and then import them in a single pdf. If you're interested in using the bitmap images, you can fetch them in tmpDir()

ebecht/ebmisc documentation built on Sept. 26, 2024, 3:17 p.m.