SPER: Spatial Paired Expression Ratio

plotSPER

R Documentation

Visualize SPER scores of a gene/cell-type pair

Description

Generate a series of plots of SDGs discovered by 'findSDG': 1) the SPER curve of the indicated pair; 2) the expression level of the gene in scRNA-seq reference data; 3) a spatial map showing the spatial of both the gene and the cell type is also generated.

Usage

plotSPER(
  cell.type,
  gene.id,
  SPER.score = NULL,
  cell.thershold = 0.3,
  min.expr = 1,
  coord,
  ST.data,
  CoDa.data,
  reference.data,
  SPER.data,
  dist.list,
  plot.dir = "./Plots/",
  save.plots = F
)

Arguments

`cell.type`	Cell Type Name
`gene.id`	Gene ID
`SPER.score`	SPER score shown in the plot title
`cell.thershold`	Threshold for the proportion of given cell type; spots whose value larger than this threshold will be marked in the spatial map
`min.expr`	Minimal expression value to plot (integer); only spots with given gene's expression greater than this value will be plotted
`coord`	Spatial coordinates for 'gg_gene'
`ST.data`	Spatial transcriptomics data, used for the spatial map of the gene's expression
`CoDa.data`	Cell-type spatial compositional data, used for the spatial map of cell-type distribution
`reference.data`	scRNA-seq reference; should be a Seurat object
`SPER.data`	SPER list to plot the SPER curve
`dist.list`	A vector containing the list of desired distance values
`plot.dir`	Directory to save the plots
`save.plots`	Whether save plots as files or return them as objects; default is FALSE, which returns plots as objects