cellProximitySpatPlot: cellProximitySpatPlot

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

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

Usage

cellProximitySpatPlot(gobject, ...)

Arguments

gobject

giotto object

...

Arguments passed on to cellProximitySpatPlot2D 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 color for cells (see details) cell_color_code named vector with colors color_as_factor convert color column to factor 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 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 show plots return_plot return ggplot object save_plot directly save the plot [boolean] save_param list of saving parameters from all_plots_save_function default_save_name default save name for saving, don't change, change save_name in save_param

Details

Description of parameters.

Value

ggplot

See Also

cellProximitySpatPlot2D and cellProximitySpatPlot3D for 3D

Examples

    cellProximitySpatPlot(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.