spatCellPlot

Visualize cells according to spatial coordinates

spatCellPlot(...)

Arguments

...

Arguments passed on to spatCellPlot2D

gobject: giotto object
show_image: show a tissue background image
gimage: a giotto image
image_name: name of a giotto image
sdimx: x-axis dimension name (default = 'sdimx')
sdimy: y-axis dimension name (default = 'sdimy')
spat_enr_names: names of spatial enrichment results to include
cell_annotation_values: numeric cell annotation columns
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
point_shape: shape of points (border, no_border or voronoi)
point_size: size of point (cell)
point_alpha: transparancy of spatial points
point_border_col: color of border around points
point_border_stroke: stroke size of border around points
show_cluster_center: plot center of selected clusters
show_center_label: plot label of selected clusters
center_point_size: size of center points
center_point_border_col: border color of center points
center_point_border_stroke: border stroke size of center points
label_size: size of labels
label_fontface: font of labels
show_network: show underlying spatial network
spatial_network_name: name of spatial network to use
network_color: color of spatial network
network_alpha: alpha of spatial network
show_grid: show spatial grid
spatial_grid_name: name of spatial grid to use
grid_color: color of spatial grid
show_other_cells: display not selected cells
other_cell_color: color of not selected cells
other_point_size: point size of not selected cells
other_cells_alpha: alpha of not selected cells
coord_fix_ratio: fix ratio between x and y-axis
show_legend: show legend
legend_text: size of legend text
legend_symbol_size: size of legend symbols
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
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 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)

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

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

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

Arguments

Value

Details

See also

Examples