Plot dimension reduction 2D#

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Last Updated: Mar 11, 2023

Description#

Visualize cells according to dimension reduction coordinates

Usage#

dimPlot2D(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  group_by = NULL,
  group_by_subset = NULL,
  dim_reduction_to_use = "umap",
  dim_reduction_name = NULL,
  dim1_to_use = 1,
  dim2_to_use = 2,
  spat_enr_names = NULL,
  show_NN_network = FALSE,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  cell_color = NULL,
  color_as_factor = TRUE,
  cell_color_code = NULL,
  cell_color_gradient = c("blue", "white", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  show_other_cells = TRUE,
  other_cell_color = "lightgrey",
  other_point_size = 0.5,
  show_cluster_center = FALSE,
  show_center_label = TRUE,
  center_point_size = 4,
  center_point_border_col = "black",
  center_point_border_stroke = 0.1,
  label_size = 4,
  label_fontface = "bold",
  edge_alpha = NULL,
  point_shape = c("border", "no_border"),
  point_size = 1,
  point_alpha = 1,
  point_border_col = "black",
  point_border_stroke = 0.1,
  title = NULL,
  show_legend = TRUE,
  legend_text = 10,
  legend_symbol_size = 2,
  background_color = "white",
  axis_text = 8,
  axis_title = 8,
  cow_n_col = NULL,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h",
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "dimPlot2D"
)

Arguments#

`gobject`	giotto object
`spat_unit`	spatial unit
`feat_type`	feature type
`group_by`	create multiple plots based on cell annotation column
`group_by_subset`	subset the group_by factor column
`dim_reduction_to_use`	dimension reduction to use
`dim_reduction_name`	dimension reduction name
`dim1_to_use`	dimension to use on x-axis
`dim2_to_use`	dimension to use on y-axis
`spat_enr_names`	names of spatial enrichment results to include
`show_NN_network`	show underlying NN network
`nn_network_to_use`	type of NN network to use (kNN vs sNN)
`network_name`	name of NN network to use, if show_NN_network = TRUE
`cell_color`	color for cells (see details)
`color_as_factor`	convert color column to factor
`cell_color_code`	named vector with colors
`cell_color_gradient`	vector with 3 colors for numeric data
`gradient_midpoint`	midpoint for color gradient
`gradient_limits`	vector with lower and upper limits
`select_cell_groups`	select subset of cells/clusters based on cell_color parameter
`select_cells`	select subset of cells based on cell IDs
`show_other_cells`	display not selected cells
`other_cell_color`	color of not selected cells
`other_point_size`	size of not selected cells
`show_cluster_center`	plot center of selected clusters
`show_center_label`	plot label of selected clusters
`center_point_size`	size of center points
`center_point_border_col`	border color of center points
`center_point_border_stroke`	border stroke size of center points
`label_size`	size of labels
`label_fontface`	font of labels
`edge_alpha`	column to use for alpha of the edges
`point_shape`	point with border or not (border or no_border)
`point_size`	size of point (cell)
`point_alpha`	transparancy of point
`point_border_col`	color of border around points
`point_border_stroke`	stroke size of border around points
`title`	title for plot, defaults to cell_color parameter
`show_legend`	show legend
`legend_text`	size of legend text
`legend_symbol_size`	size of legend symbols
`background_color`	color of plot background
`axis_text`	size of axis text
`axis_title`	size of axis title
`cow_n_col`	cowplot param: how many columns
`cow_rel_h`	cowplot param: relative heights of rows (e.g. c(1,2))
`cow_rel_w`	cowplot param: relative widths of columns (e.g. c(1,2))
`cow_align`	cowplot param: how to align
`show_plot`	show plot
`return_plot`	return ggplot object
`save_plot`	directly save the plot [boolean]
`save_param`	list of saving parameters, see `showSaveParameters`
`default_save_name`	default save name for saving, don’t change, change save_name in save_param

Details#

Description of parameters. For 3D plots see dimPlot3D

Value#

ggplot

See Also#

Other reduced dimension visualizations: dimPlot3D(), dimPlot(), plotPCA_2D(), plotPCA_3D(), plotPCA(), plotTSNE_2D(), plotTSNE_3D(), plotTSNE(), plotUMAP_2D(), plotUMAP_3D(), plotUMAP()