plot_umap: Plot function that display a Umap of scaled intensities for...

In maximemeylan/Excyte: Exhaustive eXploration of CYTometry data

Description

Plot function that display a Umap of scaled intensities for event

Usage

plot_umap(
  umap_2D,
  processed_fcs_df,
  channels = c("channels_used", "all", "with_desc")[1],
  cut_top_99th = T,
  title = c("both", "marker", "channel")[1],
  alpha = 0.5
)

Arguments

umap_2D	matrix detailing coordinates of each event on the umap
processed_fcs_df	dataframe of processed intensities for each event and informations of channel used as attribute
channels	vector of channels to select. Can be "all" to select all channels, "with_desc" to select channels with a marker description or a vector a channels
cut_top_99th	boolean value indicating if the top 1 percent should be removed to compute color scaling
alpha	numeric indicating the transparency level when plotting the umap

maximemeylan/Excyte documentation built on Nov. 10, 2020, 9:06 p.m.