spatGenePlot2D: spatGenePlot2D

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

spatGenePlot2D

Description

Visualize cells and gene expression according to spatial coordinates

Usage

spatGenePlot2D(gobject, genes, default_save_name = "spatGenePlot2D", ...)

Arguments

gobject	giotto object
genes	genes to show
default_save_name	default save name for saving, don't change, change save_name in save_param
...	Arguments passed on to spatFeatPlot2D feat_type feature type spat_unit spatial unit show_image show a tissue background image gimage a giotto image image_name name of a giotto image or multiple images if group_by largeImage_name name of a giottoLargeImage or multiple images if group by spat_loc_name name of spatial locations group_by create multiple plots based on cell annotation column group_by_subset subset the group_by factor column sdimx x-axis dimension name (default = 'sdimx') sdimy y-axis dimension name (default = 'sdimy') expression_values gene expression values to use order order points according to feature expression 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 coord_fix_ratio fix ratio between x and y-axis (default = 1) 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

Details

Description of parameters, see spatFeatPlot2D

Value

ggplot

See Also

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.