spatDimPlot

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Last Updated: Mar 11, 2023

Description

Visualize cells according to spatial AND dimension reduction coordinates 2D

Usage

spatDimPlot(...)

Arguments

...

Arguments passed on to spatDimPlot2D gobject giotto object spat_unit spatial unit feat_type feature type show_image show a tissue background image gimage a giotto image image_name name of a giotto image largeImage_name name of a giottoLargeImage spat_loc_name name of spatial locations plot_alignment direction to align plot 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 spat_enr_names names of spatial enrichment results to include 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 dim_point_shape point with border or not (border or no_border) dim_point_size size of points in dim. reduction space dim_point_alpha transparancy of point in dim. reduction space 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 center point spat_center_point_border_col border color of spatial center points ``spat_center_point_border_stroke `` border strike size of 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) network_name name of NN network to use, if show_NN_network = TRUE nn_network_alpha column to use for alpha of the edges show_spatial_network show spatial network spat_network_name name of spatial network to use spat_network_color color of spatial network spat_network_alpha alpha of spatial network show_spatial_grid show spatial grid spat_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 dim_show_legend show legend of dimension reduction plot spat_show_legend show legend of spatial plot 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

spatDimPlot2D and spatDimPlot3D for 3D visualization.

Other spatial and dimension reduction visualizations: spatDimPlot2D(), spatDimPlot3D()