spatDimCellPlot: spatDimCellPlot

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

spatDimCellPlot

Description

Visualize numerical features of cells according to spatial AND dimension reduction coordinates in 2D

Usage

spatDimCellPlot(...)

Arguments

...

Arguments passed on to spatDimCellPlot2D gobject giotto object show_image show a tissue background image gimage a giotto image image_name name of a giotto image plot_alignment direction to align plot spat_enr_names names of spatial enrichment results to include cell_annotation_values numeric cell annotation columns 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 sdimx = spatial dimension to use on x-axis sdimy = spatial dimension to use on y-axis 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 dim_point_shape dim reduction points with border or not (border or no_border) dim_point_size size of points in dim. reduction space dim_point_alpha transparancy of dim. reduction points dim_point_border_col border color of points in dim. reduction space dim_point_border_stroke border stroke of points in dim. reduction space spat_point_shape shape of points (border, no_border or voronoi) spat_point_size size of spatial points spat_point_alpha transparancy of spatial points spat_point_border_col border color of spatial points spat_point_border_stroke border stroke of spatial points dim_show_cluster_center show the center of each cluster dim_show_center_label provide a label for each cluster dim_center_point_size size of the center point dim_center_point_border_col border color of center point dim_center_point_border_stroke stroke size of center point dim_label_size size of the center label dim_label_fontface font of the center label spat_show_cluster_center show the center of each cluster spat_show_center_label provide a label for each cluster spat_center_point_size size of the spatial center points spat_center_point_border_col border color of the spatial center points spat_center_point_border_stroke stroke size of the spatial center points spat_label_size size of the center label spat_label_fontface font of the center label show_NN_network show underlying NN network nn_network_to_use type of NN network to use (kNN vs sNN) nn_network_name name of NN network to use, if show_NN_network = TRUE dim_edge_alpha column to use for alpha of the edges spat_show_network show spatial network spatial_network_name name of spatial network to use spat_network_color color of spatial network spat_network_alpha alpha of spatial network spat_show_grid show spatial grid spatial_grid_name name of spatial grid to use spat_grid_color color of spatial grid show_other_cells display not selected cells other_cell_color color of not selected cells dim_other_point_size size of not selected dim cells spat_other_point_size size of not selected spat cells spat_other_cells_alpha alpha of not selected spat cells coord_fix_ratio ratio for coordinates 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 legend_symbol_size size of legend symbols dim_background_color background color of points in dim. reduction space spat_background_color background color of spatial points 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 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

Details

Description of parameters.

Value

ggplot

See Also

Other spatial and dimension reduction cell annotation visualizations: spatDimCellPlot2D()

Examples

data(mini_giotto_single_cell)

# combine all metadata
combineMetadata(mini_giotto_single_cell, spat_enr_names = 'cluster_metagene')

# visualize total expression information
spatDimCellPlot(mini_giotto_single_cell, cell_annotation_values = 'total_expr')

# visualize enrichment results
spatDimCellPlot(mini_giotto_single_cell,
                spat_enr_names = 'cluster_metagene',
                cell_annotation_values = c('1','2'))

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