spatGenePlot: spatGenePlot

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

spatGenePlot

Description

Visualize cells and gene expression according to spatial coordinates

Usage

spatGenePlot(...)

Arguments

...

Arguments passed on to spatGenePlot2D gobject giotto object show_image show a tissue background image gimage a giotto image image_name name of a giotto image sdimx x-axis dimension name (default = 'sdimx') sdimy y-axis dimension name (default = 'sdimy') expression_values gene expression values to use genes genes to show cell_color_gradient vector with 3 colors for numeric data gradient_midpoint midpoint for color gradient gradient_limits vector with lower and upper limits show_network show underlying spatial network network_color color of spatial network spatial_network_name name of spatial network to use edge_alpha alpha of edge show_grid show spatial grid grid_color color of spatial grid spatial_grid_name name of spatial grid to use midpoint expression midpoint scale_alpha_with_expression scale expression with ggplot alpha parameter point_shape shape of points (border, no_border or voronoi) point_size size of point (cell) point_alpha transparancy of points point_border_col color of border around points point_border_stroke stroke size of border around points cow_n_col cowplot param: how many columns cow_rel_h cowplot param: relative height cow_rel_w cowplot param: relative width cow_align cowplot param: how to align show_legend show legend legend_text size of legend text background_color color of plot background vor_border_color border colorr for voronoi plot vor_max_radius maximum radius for voronoi 'cells' vor_alpha transparancy of voronoi 'cells' axis_text size of axis text axis_title size of axis title show_plot show plots 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.

Value

ggplot

See Also

spatGenePlot3D and spatGenePlot2D

Other spatial gene expression visualizations: spatGenePlot2D(), spatGenePlot3D()

Examples

data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1:2]
spatGenePlot(mini_giotto_single_cell, genes = selected_genes, point_size = 3)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.