Dimension reduction plot
Arguments
- object
A seurat object
- reduction
Name of the reduction to plot (for example, "umap").
- graph
Specify the graph name to add edges between cell neighbors to the plot.
- group_by
A character vector of column name(s) to group the data. Default is NULL.
- ...
Other arguments passed to
plotthis::DimPlot().
Examples
# \donttest{
data(pancreas_sub)
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP")
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
theme = "theme_blank")
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
palette = "seurat", theme = "theme_blank")
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
theme = ggplot2::theme_classic, theme_args = list(base_size = 16))
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
raster = TRUE, raster_dpi = 30)
# Highlight cells
CellDimPlot(pancreas_sub,
group_by = "SubCellType", reduction = "UMAP",
highlight = 'SubCellType == "Epsilon"'
)
CellDimPlot(pancreas_sub,
group_by = "SubCellType", split_by = "Phase", reduction = "UMAP",
highlight = TRUE, theme = "theme_blank", legend.position = "none"
)
CellDimPlot(pancreas_sub,
group_by = "SubCellType", facet_by = "Phase", reduction = "UMAP",
highlight = TRUE, theme = "theme_blank", legend.position = "none"
)
# Add group labels
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
label = TRUE)
CellDimPlot(pancreas_sub,
group_by = "SubCellType", reduction = "UMAP",
label = TRUE, label_fg = "orange", label_bg = "red", label_size = 5
)
CellDimPlot(pancreas_sub,
group_by = "SubCellType", reduction = "UMAP",
label = TRUE, label_insitu = TRUE
)
CellDimPlot(pancreas_sub,
group_by = "SubCellType", reduction = "UMAP",
label = TRUE, label_insitu = TRUE, label_repel = TRUE,
label_segment_color = "red"
)
# Add various shape of marks
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
add_mark = TRUE)
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
add_mark = TRUE, mark_expand = grid::unit(1, "mm"))
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
add_mark = TRUE, mark_alpha = 0.3)
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
add_mark = TRUE, mark_linetype = 2)
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
add_mark = TRUE, mark_type = "ellipse")
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
add_mark = TRUE, mark_type = "rect")
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
add_mark = TRUE, mark_type = "circle")
# Add a density layer
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
add_density = TRUE)
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
add_density = TRUE, density_filled = TRUE)
#> Warning: Removed 396 rows containing missing values or values outside the scale range
#> (`geom_raster()`).
#> Warning: Removed 396 rows containing missing values or values outside the scale range
#> (`geom_raster()`).
CellDimPlot(pancreas_sub,
group_by = "SubCellType", reduction = "UMAP",
add_density = TRUE, density_filled = TRUE, density_filled_palette = "Blues",
highlight = TRUE
)
#> Warning: Removed 396 rows containing missing values or values outside the scale range
#> (`geom_raster()`).
#> Warning: Removed 396 rows containing missing values or values outside the scale range
#> (`geom_raster()`).
# Add statistical charts
CellDimPlot(pancreas_sub,
group_by = "CellType", reduction = "UMAP", stat_by = "Phase")
CellDimPlot(pancreas_sub,
group_by = "CellType", reduction = "UMAP", stat_by = "Phase",
stat_plot_type = "ring", stat_plot_label = TRUE, stat_plot_size = 0.15)
CellDimPlot(pancreas_sub,
group_by = "CellType", reduction = "UMAP", stat_by = "Phase",
stat_plot_type = "bar", stat_type = "count")
CellDimPlot(pancreas_sub,
group_by = "CellType", reduction = "UMAP", stat_by = "Phase",
stat_plot_type = "line", stat_type = "count", stat_args = list(point_size = 1))
# Chane the plot type from point to the hexagonal bin
CellDimPlot(pancreas_sub, group_by = "CellType", reduction = "UMAP",
hex = TRUE)
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`geom_hex()`).
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`geom_hex()`).
CellDimPlot(pancreas_sub, group_by = "CellType", reduction = "UMAP",
hex = TRUE, hex_bins = 20)
#> Warning: Removed 4 rows containing missing values or values outside the scale range
#> (`geom_hex()`).
#> Warning: Removed 4 rows containing missing values or values outside the scale range
#> (`geom_hex()`).
CellDimPlot(pancreas_sub, group_by = "CellType", reduction = "UMAP",
hex = TRUE, hex_count = FALSE)
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`geom_hex()`).
#> Warning: Removed 5 rows containing missing values or values outside the scale range
#> (`geom_hex()`).
# Show neighbors graphs on the plot
CellDimPlot(pancreas_sub, group_by = "CellType", reduction = "UMAP",
graph = "RNA_nn")
CellDimPlot(pancreas_sub, group_by = "CellType", reduction = "UMAP",
graph = "RNA_snn", edge_color = "grey80")
# Show lineages on the plot based on the pseudotime
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
lineages = paste0("Lineage", 1:3))
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_path()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_path()`).
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
lineages = paste0("Lineage", 1:3), lineages_whiskers = TRUE)
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_path()`).
#> Warning: Removed 8 rows containing missing values or values outside the scale range
#> (`geom_path()`).
CellDimPlot(pancreas_sub, group_by = "SubCellType", reduction = "UMAP",
lineages = paste0("Lineage", 1:3), lineages_span = 0.1)
# }