`spatGenePlot`¶

spatGenePlot

Description¶

Visualize cells and gene expression according to spatial coordinates

Usage¶

spatGenePlot(...)

Arguments¶

Argument

Description

...

Arguments passed on to ``spatGenePlot2D` <#spatgeneplot2d>`_ list(“n”, ” “, list(list(list(“gobject”)), list(“giotto object”)), “n”, ” “, list(list(list(“show_image”)), list(“show a tissue background image”)), “n”, ” “, list(list(list(“gimage”)), list(“a giotto image”)), “n”, ” “, list(list(list(“image_name”)), list(“name of a giotto image”)), “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("expression_values")), list("gene expression values to use")), "\n", "    ", list(list(list("genes")), list("genes to show")), "\n", "    ", list(list(list("cell_color_gradient")), list("vector with 3 colors for numeric data")), "\n", "    ", list(list(list("gradient_midpoint")), list("midpoint for color gradient")), "\n", "    ", list(list(list("gradient_limits")), list("vector with lower and upper limits")), "\n", "    ", list(list(list("show_network")), list("show underlying spatial network")),
"\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("edge_alpha")), list("alpha of edge")), "\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("midpoint")), list("expression midpoint")), "\n", "    ", list(list(list("scale_alpha_with_expression")), list("scale expression with ggplot alpha parameter")), "\n", "    ", list(list(list("point_shape")), list("shape of points (border, no_border or voronoi)")), "\n", "    ", list(list(list("point_size")), list("size of point (cell)")), "\n", "    ", list(list(list("point_alpha")), list("transparancy of points")), "\n", "    ", list(list(list("point_border_col")), list("color of border around points")),
"\n", "    ", list(list(list("point_border_stroke")), list("stroke size of border around points")), "\n", "    ", list(list(list("cow_n_col")), list("cowplot param: how many columns")), "\n", "    ", list(list(list("cow_rel_h")), list("cowplot param: relative height")), "\n", "    ", list(list(list("cow_rel_w")), list("cowplot param: relative width")), "\n", "    ", list(list(list("cow_align")), list("cowplot param: how to align")), "\n", "    ", list(list(list("show_legend")), list("show legend")),
"\n", "    ", list(list(list("legend_text")), list("size of legend text")), "\n", "    ", list(list(list("background_color")), list("color of plot background")), "\n", "    ", list(list(list("vor_border_color")), list("border colorr for voronoi plot")), "\n", "    ", list(list(list("vor_max_radius")), list("maximum radius for voronoi 'cells'")), "\n", "    ", list(list(list("vor_alpha")), list("transparancy of voronoi 'cells'")), "\n", "    ", list(list(list("axis_text")), list("size of axis text")),
"\n", "    ", list(list(list("axis_title")), list("size of axis title")), "\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, see ", list(list("showSaveParameters")))), "\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¶

``spatGenePlot3D` <#spatgeneplot3d>`_ and ``spatGenePlot2D` <#spatgeneplot2d>`_

Other spatial gene expression visualizations: ``spatGenePlot2D` <#spatgeneplot2d>`_ , ``spatGenePlot3D` <#spatgeneplot3d>`_

Examples¶

data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1:2]
spatGenePlot(mini_giotto_single_cell, genes = selected_genes, point_size = 3)

spatGenePlot¶