spatDimGenePlot

Visualize cells according to spatial AND dimension reduction coordinates in ggplot mode

spatDimGenePlot(...)

Arguments

...

Arguments passed on to spatDimGenePlot2D gobject giotto object show_image show a tissue background image gimage a giotto image image_name name of a giotto image expression_values gene expression values to use plot_alignment direction to align plot genes genes to show 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 dim_point_shape dim reduction points with border or not (border or no_border) dim_point_size dim reduction plot: point size dim_point_alpha transparancy of dim. reduction points dim_point_border_col color of border around points dim_point_border_stroke stroke size of border around points show_NN_network show underlying NN network show_spatial_network show underlying spatial netwok 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 dim_network_color color of NN network dim_edge_alpha dim reduction plot: column to use for alpha of the edges scale_alpha_with_expression scale expression with ggplot alpha parameter sdimx spatial x-axis dimension name (default = 'sdimx') sdimy spatial y-axis dimension name (default = 'sdimy') spatial_network_name name of spatial network to use spatial_network_color color of spatial network show_spatial_grid show spatial grid grid_color color of spatial grid spatial_grid_name name of spatial grid to use spat_point_shape spatial points with border or not (border or no_border) spat_point_size spatial plot: point size spat_point_alpha transparancy of spatial points spat_point_border_col color of border around points spat_point_border_stroke stroke size of border around points spat_edge_alpha edge alpha 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_legend show legend legend_text size of legend text dim_background_color color of plot background for dimension plot spat_background_color color of plot background for spatial plot 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 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_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

Value

ggplot

Details

Description of parameters.

See also

spatDimGenePlot3D

Other spatial and dimension reduction gene expression visualizations: spatDimGenePlot2D(), spatDimGenePlot3D()

Examples

data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1]
spatDimGenePlot(mini_giotto_single_cell, genes = selected_genes,
                 dim_point_size = 3, spat_point_size = 3,
                 cow_n_col = 1, plot_alignment = 'horizontal')