PlotTSNE: Creates tsne plot

In quon-titative-biology/scAlign: An alignment and integration method for single cell genomics

Description

Helper function to plot aligned data from the results of running scAlign().

Usage

PlotTSNE(
  object,
  data.use,
  labels.use = "scAlign.labels",
  cols = NULL,
  title = "",
  legend = "none",
  point.size = 3,
  seed = 1234,
  ...
)

Arguments

object	scAlign class object with aligned data
data.use	Specifies which alignment results to use.
labels.use	Specifies "dataset" or "celltype" labeling from object meta.data.
cols	Colours for plot
title	ggplot title
legend	Determines if legend should be drawn
point.size	Size of geom_point
seed	Random seed for reproducability
...	Additional arguments to Rtsne function
labels	Object labels

Value

ggplot2 object

Examples

 library(SingleCellExperiment)

 ## Input data, 1000 genes x 100 cells
 data = matrix( rnorm(1000*100,mean=0,sd=1), 1000, 100)
 rownames(data) = paste0("gene", seq_len(1000))
 colnames(data) = paste0("cell", seq_len(100))

 age    = c(rep("young",50), rep("old",50))
 labels = c(c(rep("type1",25), rep("type2",25)), c(rep("type1",25), rep("type2",25)))

 ctrl.data = data[,which(age == "young")]
 stim.data = data[,which(age == "old")]

 ## Build the SCE object for input to scAlign using Seurat preprocessing and variable gene selection
 ctrlSCE <- SingleCellExperiment(
               assays = list(scale.data = data[,which(age == "young")]))

 stimSCE <- SingleCellExperiment(
               assays = list(scale.data = data[,which(age == "old")]))

 ## Build the scAlign class object and compute PCs
 scAlignHSC = scAlignCreateObject(sce.objects = list("YOUNG"=ctrlSCE,
                                                     "OLD"=stimSCE),
                                  labels = list(labels[which(age == "young")],
                                                labels[which(age == "old")]),
                                  pca.reduce = FALSE,
                                  cca.reduce = FALSE,
                                  project.name = "scAlign_Kowalcyzk_HSC")

 ## Run scAlign with high_var_genes
 scAlignHSC = scAlign(scAlignHSC,
                    options=scAlignOptions(steps=100,
                                           log.every=100,
                                           norm=TRUE,
                                           early.stop=FALSE),
                    encoder.data="scale.data",
                    supervised='none',
                    run.encoder=TRUE,
                    run.decoder=FALSE,
                    log.results=FALSE,
                    log.dir=file.path(tempdir(),'gene_input'),
                    device="CPU")

 ## Plot alignment for 3 input types
 example_plot = PlotTSNE(scAlignHSC,
                           "ALIGNED-GENE",
                           "scAlign.labels",
                           title="scAlign-Gene",
                           perplexity=30)

quon-titative-biology/scAlign documentation built on Nov. 17, 2021, 9:57 a.m.