Visualize 2D cell-cell interactions according to spatial coordinates in ggplot mode
cellProximitySpatPlot2D(
gobject,
interaction_name = NULL,
cluster_column = NULL,
sdimx = "sdimx",
sdimy = "sdimy",
cell_color = NULL,
cell_color_code = NULL,
color_as_factor = T,
show_other_cells = F,
show_network = F,
show_other_network = F,
network_color = NULL,
spatial_network_name = "Delaunay_network",
show_grid = F,
grid_color = NULL,
spatial_grid_name = "spatial_grid",
coord_fix_ratio = 1,
show_legend = T,
point_size_select = 2,
point_select_border_col = "black",
point_select_border_stroke = 0.05,
point_size_other = 1,
point_alpha_other = 0.3,
point_other_border_col = "lightgrey",
point_other_border_stroke = 0.01,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "cellProximitySpatPlot2D"
)giotto object
cell-cell interaction name
cluster column with cell clusters
x-axis dimension name (default = 'sdimx')
y-axis dimension name (default = 'sdimy')
color for cells (see details)
named vector with colors
convert color column to factor
decide if show cells not in network
show spatial network of selected cells
show spatial network of not selected cells
color of spatial network
name of spatial network to use
show spatial grid
color of spatial grid
name of spatial grid to use
fix ratio between x and y-axis
show legend
size of selected points
border color of selected points
stroke size of selected points
size of other points
opacity of other points
border color of other points
stroke size of other points
show plots
return ggplot object
directly save the plot [boolean]
list of saving parameters from all_plots_save_function
default save name for saving, don't change, change save_name in save_param
ggplot
Description of parameters.