plot_params: plot_params
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

plot_params

R Documentation

plot_params

Description

plot_params

Arguments

`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 for not selected cells
`other_point_size`	point size for 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
`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
`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`	transparency of points
`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