spatPlot: spatPlot

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Visualize cells according to spatial coordinates

Usage

spatPlot(...)

Arguments

...

Arguments passed on to spatPlot2D gobject giotto object show_image show a tissue background image gimage a giotto image image_name name of a giotto image group_by create multiple plots based on cell annotation column group_by_subset subset the group_by factor column sdimx x-axis dimension name (default = 'sdimx') sdimy y-axis dimension name (default = 'sdimy') spat_enr_names names of spatial enrichment results to include cell_color color for cells (see details) color_as_factor convert color column to factor cell_color_code named vector with colors cell_color_gradient vector with 3 colors for numeric data gradient_midpoint midpoint for color gradient gradient_limits vector with lower and upper limits select_cell_groups select subset of cells/clusters based on cell_color parameter select_cells select subset of cells based on cell IDs point_shape shape of points (border, no_border or voronoi) point_size size of point (cell) point_alpha transparancy of point point_border_col color of border around points point_border_stroke stroke size of border around points show_cluster_center plot center of selected clusters show_center_label plot label of selected clusters center_point_size size of center points center_point_border_col border color of center points center_point_border_stroke border stroke size of center points label_size size of labels label_fontface font of labels show_network show underlying spatial network spatial_network_name name of spatial network to use network_color color of spatial network network_alpha alpha of spatial network show_grid show spatial grid spatial_grid_name name of spatial grid to use grid_color color of spatial grid show_other_cells display not selected cells other_cell_color color of not selected cells other_point_size point size of not selected cells other_cells_alpha alpha of not selected cells coord_fix_ratio fix ratio between x and y-axis title title of plot show_legend show legend legend_text size of legend text legend_symbol_size size of legend symbols background_color color of plot background vor_border_color border colorr for voronoi plot vor_max_radius maximum radius for voronoi 'cells' vor_alpha transparancy of voronoi 'cells' axis_text size of axis text axis_title size of axis title cow_n_col cowplot param: how many columns cow_rel_h cowplot param: relative height cow_rel_w cowplot param: relative width cow_align cowplot param: how to align show_plot show plot return_plot return ggplot object save_plot directly save the plot [boolean] 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

Details

Description of parameters.

Value

ggplot

See Also

spatPlot3D

Other spatial visualizations: spatPlot2D(), spatPlot3D()

Examples

    spatPlot(gobject)

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