ProjectionPlot: Projection Plot

In zh542370159/SCP: Single Cell Pipeline

Projection Plot

Description

This function generates a projection plot, which can be used to compare two groups of cells in a dimensionality reduction space.

Usage

ProjectionPlot(
  srt_query,
  srt_ref,
  query_group = NULL,
  ref_group = NULL,
  query_reduction = "ref.embeddings",
  ref_reduction = srt_query[[query_reduction]]@misc[["reduction.model"]] %||% NULL,
  query_param = list(palette = "Set1", cells.highlight = TRUE),
  ref_param = list(palette = "Paired"),
  xlim = NULL,
  ylim = NULL,
  pt.size = 0.8,
  stroke.highlight = 0.5
)

Arguments

srt_query	An object of class Seurat storing the query group cells.
srt_ref	An object of class Seurat storing the reference group cells.
query_group	The grouping variable for the query group cells.
ref_group	The grouping variable for the reference group cells.
query_reduction	The name of the reduction in the query group cells.
ref_reduction	The name of the reduction in the reference group cells.
query_param	A list of parameters for customizing the query group plot. Available parameters: palette (color palette for groups) and cells.highlight (whether to highlight cells).
ref_param	A list of parameters for customizing the reference group plot. Available parameters: palette (color palette for groups) and cells.highlight (whether to highlight cells).
xlim	The x-axis limits for the plot. If not provided, the limits will be calculated based on the data.
ylim	The y-axis limits for the plot. If not provided, the limits will be calculated based on the data.
pt.size	The size of the points in the plot.
stroke.highlight	The size of the stroke highlight for cells.

Examples

data("panc8_sub")
srt_ref <- panc8_sub[, panc8_sub$tech != "fluidigmc1"]
srt_query <- panc8_sub[, panc8_sub$tech == "fluidigmc1"]
srt_ref <- Integration_SCP(srt_ref, batch = "tech", integration_method = "Seurat")
CellDimPlot(srt_ref, group.by = c("celltype", "tech"))

# Projection
srt_query <- RunKNNMap(srt_query = srt_query, srt_ref = srt_ref, ref_umap = "SeuratUMAP2D")
ProjectionPlot(srt_query = srt_query, srt_ref = srt_ref, query_group = "celltype", ref_group = "celltype")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.