spatDimCellPlot

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

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

Value

ggplot

Details

Description of parameters.

Examples


data(mini_giotto_single_cell)
#> Warning: data set ‘mini_giotto_single_cell’ not found

# combine all metadata
combineMetadata(mini_giotto_single_cell, spat_enr_names = 'cluster_metagene')
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found

# visualize total expression information
spatDimCellPlot(mini_giotto_single_cell, cell_annotation_values = 'total_expr')
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found

# visualize enrichment results
spatDimCellPlot(mini_giotto_single_cell,
                spat_enr_names = 'cluster_metagene',
                cell_annotation_values = c('1','2'))
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Warning: restarting interrupted promise evaluation
#> Error: object 'mini_giotto_single_cell' not found

Arguments

Value

Details

See also

Examples