cellProximitySpatPlot

Visualize 2D cell-cell interactions according to spatial coordinates in ggplot mode

cellProximitySpatPlot(gobject, ...)

Arguments

gobject

giotto object

...

Arguments passed on to cellProximitySpatPlot2D

spat_loc_name: spatial locations to use
interaction_name: cell-cell interaction name
cluster_column: cluster column with cell clusters
sdimx: x-axis dimension name (default = 'sdimx')
sdimy: y-axis dimension name (default = 'sdimy')
show_other_cells: decide if show cells not in network
show_network: show spatial network of selected cells
show_other_network: show spatial network of not selected cells
network_color: color of spatial network
show_grid: show spatial grid
grid_color: color of spatial grid
spatial_grid_name: name of spatial grid to use
coord_fix_ratio: fix ratio between x and y-axis
point_size_select: size of selected points
point_select_border_col: border color of selected points
point_select_border_stroke: stroke size of selected points
point_size_other: size of other points
point_alpha_other: opacity of other points
point_other_border_col: border color of other points
point_other_border_stroke: stroke size of other points
spat_unit: spatial unit (e.g. "cell")
feat_type: feature type (e.g. "rna", "dna", "protein")
show_plot: logical. show plot
return_plot: logical. return ggplot object
save_plot: logical. save the plot
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
cell_color: character. what to color cells by (e.g. metadata col or spatial enrichment col)
color_as_factor: logical. convert color column to factor. discrete colors are used when this is TRUE. continuous colors when FALSE.
cell_color_code: character. discrete colors to use. palette to use or named vector of colors
spatial_network_name: name of spatial network to use
show_legend: logical. show legend

Value

ggplot

Details

Description of parameters.

Arguments

Value

Details

See also