PlotSickleJrUMAP {jrSiCKLSNMF}

Generate UMAP plots for an object of class SickleJr

Description

Plot the first and second dimensions of a UMAP dimension reduction and color either by clustering results or metadata.

Usage

PlotSickleJrUMAP(
  SickleJr,
  umap.modality = "H",
  cluster = "kmeans",
  title = "",
  colorbymetadata = NULL,
  legendname = NULL
)

Arguments

SickleJr

An object of class SickleJr

umap.modality

String corresponding to the name of the UMAP of interest: defaults to "H"

cluster

String input that indicates which cluster to color by: defaults to "kmeans"

title

String input for optional ggplot2{ggplot} plot title

colorbymetadata

Name of metadata column if coloring by metadata

legendname

String input that to allow specification of a different legend name

Value

An object of class SickleJr with plots added to the plots slot

References

Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis, 2 edition. Springer International Publishing, Cham, Switzerland. ISBN 978-3-319-24277-4, doi:10.1007/978-3-319-24277-4, https://ggplot2.tidyverse.org/.

Examples

SimSickleJrSmall<-PlotSickleJrUMAP(SimSickleJrSmall,
title="K-Means Example")
SimSickleJrSmall<-PlotSickleJrUMAP(SimSickleJrSmall,umap.modality=1)