cellProximitySpatPlot#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L2864

Description#

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

Usage#

cellProximitySpatPlot(gobject, ...)

Arguments#

Argument

Description

gobject

giotto object

...

Arguments passed on to `cellProximitySpatPl ot2D <#cellproximityspatplot2d>`__ list(“?, ? “, list(list(list(?feat_type?)), list(“feature type?)), “?, ? “, list(list(list(?spat_unit?)), list(“spatial unit?)), “?, ? “, list(list(list(?spat_loc_name?)), list(“spatial locations to use?)), “?, ? “, list(list(list(?interaction_name?)), list(“cell-cell interaction name?)), “?, ? “, list(list(list(?cluster_column?)), list(“cluster column with cell clusters?)), “?, ? “, list(list(list(?sdimx?)), list(“x-axis dimension name (default = ‘sdimx’)?)), “?,

"    ", list(list(list("sdimy")), list("y-axis dimension name (default = 'sdimy')")), "\n", "    ", list(list(list("cell_color")), list("color for cells (see details)")), "\n", "    ", list(list(list("cell_color_code")), list("named vector with colors")), "\n", "    ", list(list(list("color_as_factor")), list("convert color column to factor")), "\n", "    ", list(list(list("show_other_cells")), list("decide if show cells not in network")), "\n", "    ", list(list(list("show_network")), list("show spatial network of selected cells")),
"\n", "    ", list(list(list("show_other_network")), list("show spatial network of not selected cells")), "\n", "    ", list(list(list("network_color")), list("color of spatial network")), "\n", "    ", list(list(list("spatial_network_name")), list("name of spatial network to use")), "\n", "    ", list(list(list("show_grid")), list("show spatial grid")), "\n", "    ", list(list(list("grid_color")), list("color of spatial grid")), "\n", "    ", list(list(list("spatial_grid_name")), list("name of spatial grid to use")),
"\n", "    ", list(list(list("coord_fix_ratio")), list("fix ratio between x and y-axis")), "\n", "    ", list(list(list("show_legend")), list("show legend")), "\n", "    ", list(list(list("point_size_select")), list("size of selected points")), "\n", "    ", list(list(list("point_select_border_col")), list("border color of selected points")), "\n", "    ", list(list(list("point_select_border_stroke")), list("stroke size of selected points")), "\n", "    ", list(list(list("point_size_other")),
    list("size of other points")), "\n", "    ", list(list(list("point_alpha_other")), list("opacity of other points")), "\n", "    ", list(list(list("point_other_border_col")), list("border color of other points")), "\n", "    ", list(list(list("point_other_border_stroke")), list("stroke size of other points")), "\n", "    ", list(list(list("show_plot")), list("show plots")), "\n", "    ", list(list(list("return_plot")), list("return ggplot object")), "\n", "    ", list(list(list("save_plot")),
    list("directly save the plot [boolean]")), "\n", "    ", list(list(list("save_param")), list("list of saving parameters from ", list(list("all_plots_save_function")))), "\n", "    ", list(list(list("default_save_name")), list("default save name for saving, don't change, change save_name in save_param")), "\n", "  ")

Details#

Description of parameters.

Value#

ggplot

Seealso#

`cellProximitySpatPlot2D <#cellproximityspatplot2d>`__ and `cellProximitySpatPlot3D <#cellproximityspatplot3d>`__ for 3D