plot_spat_point_layer_ggplot: plot_spat_point_layer_ggplot
In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

plot_spat_point_layer_ggplot

R Documentation

plot_spat_point_layer_ggplot

Description

creat ggplot point layer for spatial coordinates

Usage

plot_spat_point_layer_ggplot(
  ggobject,
  sdimx = NULL,
  sdimy = NULL,
  cell_locations_metadata_selected,
  cell_locations_metadata_other,
  cell_color = NULL,
  color_as_factor = T,
  cell_color_code = NULL,
  cell_color_gradient = c("blue", "white", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  point_size = 2,
  point_alpha = 1,
  point_border_col = "lightgrey",
  point_border_stroke = 0.1,
  show_cluster_center = F,
  show_center_label = T,
  center_point_size = 4,
  center_point_border_col = "black",
  center_point_border_stroke = 0.1,
  label_size = 4,
  label_fontface = "bold",
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 1,
  show_legend = TRUE
)

Arguments

`sdimx`	x-axis dimension name (default = 'sdimx')
`sdimy`	y-axis dimension name (default = 'sdimy')
`cell_locations_metadata_selected`	annotated location from selected cells
`cell_locations_metadata_other`	annotated location from non-selected cells
`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
`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
`show_cluster_center`	plot center of selected clusters
`show_center_label`	plot label of selected clusters
`center_point_size`	size of center points
`label_size`	size of labels
`label_fontface`	font of labels
`show_other_cells`	display not selected cells
`other_cell_color`	color for not selected cells
`other_point_size`	point size for not selected cells
`show_legend`	show legend
`gobject`	giotto object