Custom Feature Plot

Creates a custom feature plot for visualizing a feature's values on a reduced dimension embedding (e.g., UMAP or t-SNE).

CustomFeaturePlot(
  coord,
  value,
  reduction = NULL,
  dims = 1:2,
  value_name = NULL,
  title_name = NULL,
  order_point = TRUE
)

Arguments

coord

A Seurat object or a matrix of coordinates. If a Seurat object is provided, embeddings will be extracted from Seurat.

value

A vector of values to plot. If coord is a Seurat object, value can be a column name from coord@meta.data.

reduction

Character; the name of the reduction embedding to use (e.g., "umap", "tsne"). Default is NULL.

dims

A vector specifying which dimensions to use. Default is c(1,2).

value_name

Character; the name of the value to be used in the plot legend. Default is NULL.

title_name

Character; the title of the plot. Default is NULL.

order_point

Logical; whether to order points by value. Default is TRUE.

Value

A ggplot2 object representing the custom feature plot.

Examples

# Example with Seurat object
library(Seurat)
#> Attaching SeuratObject
seurat_obj <- CreateSeuratObject(matrix(runif(2000), nrow = 200))
#> Error in CreateAssayObject(counts = counts, min.cells = min.cells, min.features = min.features,     row.names = row.names): No cell names (colnames) names present in the input matrix
seurat_obj <- RunUMAP(seurat_obj, dims = 1:10)
#> Error in RunUMAP(seurat_obj, dims = 1:10): object 'seurat_obj' not found
seurat_obj$feature <- rnorm(200)
#> Error in seurat_obj$feature <- rnorm(200): object 'seurat_obj' not found
plot <- CustomFeaturePlot(seurat_obj, "feature", reduction = "umap", title_name = "Feature Plot")
#> Error in CustomFeaturePlot(seurat_obj, "feature", reduction = "umap",     title_name = "Feature Plot"): object 'seurat_obj' not found
print(plot)
#> function (x, y, ...) 
#> UseMethod("plot")
#> <bytecode: 0x560b60892860>
#> <environment: namespace:base>

# Example with coordinate matrix
coord <- matrix(rnorm(200), nrow = 100, ncol = 2)
value <- rnorm(100)
plot <- CustomFeaturePlot(coord, value, title_name = "Custom Plot")
#> Warning: the condition has length > 1 and only the first element will be used
#> Error in as.name(colnames(coord)[1]): invalid type/length (symbol/0) in vector allocation
print(plot)
#> function (x, y, ...) 
#> UseMethod("plot")
#> <bytecode: 0x560b60892860>
#> <environment: namespace:base>