Visualize 2D cell-cell interactions according to spatial coordinates in ggplot mode
cellProximitySpatPlot2D(
gobject,
spat_unit = NULL,
feat_type = NULL,
spat_loc_name = NULL,
interaction_name = NULL,
cluster_column = NULL,
sdimx = "sdimx",
sdimy = "sdimy",
cell_color = NULL,
cell_color_code = NULL,
color_as_factor = TRUE,
show_other_cells = FALSE,
show_network = FALSE,
show_other_network = FALSE,
network_color = NULL,
spatial_network_name = "Delaunay_network",
show_grid = FALSE,
grid_color = NULL,
spatial_grid_name = "spatial_grid",
coord_fix_ratio = 1,
show_legend = TRUE,
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 = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = "cellProximitySpatPlot2D"
)Arguments
- gobject
giotto object
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- 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')
- cell_color
character. what to color cells by (e.g. metadata col or spatial enrichment col)
- cell_color_code
character. discrete colors to use. palette to use or named vector of colors
- color_as_factor
logical. convert color column to factor. discrete colors are used when this is TRUE. continuous colors when FALSE.
- 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
- spatial_network_name
name of spatial network to use
- 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
- show_legend
logical. show legend
- 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
- 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
Value
ggplot
Details
Description of parameters.
Examples
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> cell_spatInfo_spatVector.shp
#> cell
#>
#> 3.2 read Giotto spatial centroid information
#> cell
#>
#> 3.3 read Giotto spatial overlap information
#> No overlaps were found, overlap loading will be
#> skipped
#>
#> 4. read Giotto image information
#> a giotto python environment was found
#> Using python path:
#> "/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw"
g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)
x <- cellProximityEnrichment(g, cluster_column = "leiden_clus")
cellProximitySpatPlot2D(gobject = g, cluster_column = "leiden_clus",
interaction_name = x)
