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DimPlot

Source: R/celldimplot.R
CellDimPlot.Rd

Dimension reduction plot

Usage

CellDimPlot(object, reduction = NULL, graph = NULL, ...)

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.

...

Other arguments passed to plotthis::DimPlot.

Value

A ggplot object or a list if combine is FALSE

Examples

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)