biaxial_plot: Generate a biaxial dot plot with contouring of the SCE data

In kordastilab/ImmunoCluster: Fast and accesible Immune profiling CyTOF data

Description

Generate a biaxial dot plot with contouring of the SCE data

Usage

biaxial_plot(
  indata,
  assay = "scaled",
  marker_x,
  marker_y,
  clustering = NULL,
  colkey = NULL
)

Arguments

indata	a SingleCellExperiment.
assay	the SCE assay to choose from.
marker_x	marker to display on the x axis
marker_y	marker to display on the y axis
clustering	metadata slot to colour the plot by
colkey	a list of colours matching the number of conditions found in clustering

Value

a ggplot object.

Author(s)

James Opzoomer [e-mail]

Examples

# Download complete ImmunoCluster SCE object from zenodo
sce_gvhd = readRDS(url("https://zenodo.org/record/3801882/files/sce_gvhd.rds"))

biaxial_plot(sce_gvhd, marker_x = "CD8a", marker_y = "CD4")

kordastilab/ImmunoCluster documentation built on May 10, 2021, 7:41 a.m.