`cellProximitySpatPlot`¶

cellProximitySpatPlot

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 ``cellProximitySpatPlot2D` <#cellproximityspatplot2d>`_ list(“n”, ” “, list(list(list(“interaction_name”)), list(“cell-cell interaction name”)), “n”, ” “, list(list(list(“cluster_column”)), list(“cluster column with cell clusters”)), “n”, ” “, list(list(list(“sdimx”)), list(“x-axis dimension name (default = ‘sdimx’)”)), “n”, ” “, 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

cellProximitySpatPlot¶