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

plot_point_layer_ggplot_noFILL

R Documentation

plot_point_layer_ggplot_noFILL

Description

Visualize cells in point layer according to dimension reduction coordinates without borders

Usage

plot_point_layer_ggplot_noFILL(
  ggobject,
  annotated_DT_selected,
  annotated_DT_other,
  cell_color = NULL,
  color_as_factor = T,
  cell_color_code = NULL,
  cell_color_gradient = c("blue", "white", "red"),
  gradient_midpoint = 0,
  gradient_limits = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  point_size = 1,
  point_alpha = 1,
  show_cluster_center = F,
  show_center_label = T,
  center_point_size = 4,
  label_size = 4,
  label_fontface = "bold",
  edge_alpha = NULL,
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 0.5,
  show_legend = T
)

Arguments

`annotated_DT_selected`	annotated data.table of selected cells
`annotated_DT_other`	annotated data.table of not 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
`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
`edge_alpha`	column to use for alpha of the edges
`show_other_cells`	display not selected cells
`other_cell_color`	color of not selected cells
`other_point_size`	size of not selected cells
`show_legend`	show legend
`gobject`	giotto object