spatDimCellPlot¶
spatDimCellPlot
Description¶
Visualize numerical features of cells according to spatial AND dimension reduction coordinates in 2D
Usage¶
spatDimCellPlot(...)
Arguments¶
Argument |
Description |
|---|---|
|
Arguments passed on to ``spatDimCellPlot2D` <#spatdimcellplot2d>`_ 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(“plot_alignment”)), list(“direction to align plot”)), “n”, ” “, list(list(list(“spat_enr_names”)), list(“names of spatial enrichment results to include”)), “n”, ” “, |
list(list(list("cell_annotation_values")), list("numeric cell annotation columns")), "\n", " ", list(list(list("dim_reduction_to_use")), list("dimension reduction to use")), "\n", " ", list(list(list("dim_reduction_name")), list("dimension reduction name")), "\n", " ", list(list(list("dim1_to_use")), list("dimension to use on x-axis")), "\n", " ", list(list(list("dim2_to_use")), list("dimension to use on y-axis")), "\n", " ", list(list(list("sdimx")), list("= spatial dimension to use on x-axis")),
"\n", " ", list(list(list("sdimy")), list("= spatial dimension to use on y-axis")), "\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("select_cell_groups")), list("select subset of cells/clusters based on cell_color parameter")),
"\n", " ", list(list(list("select_cells")), list("select subset of cells based on cell IDs")), "\n", " ", list(list(list("dim_point_shape")), list("dim reduction points with border or not (border or no_border)")), "\n", " ", list(list(list("dim_point_size")), list("size of points in dim. reduction space")), "\n", " ", list(list(list("dim_point_alpha")), list("transparancy of dim. reduction points")), "\n", " ", list(list(list("dim_point_border_col")), list("border color of points in dim. reduction space")),
"\n", " ", list(list(list("dim_point_border_stroke")), list("border stroke of points in dim. reduction space")), "\n", " ", list(list(list("spat_point_shape")), list("shape of points (border, no_border or voronoi)")), "\n", " ", list(list(list("spat_point_size")), list("size of spatial points")), "\n", " ", list(list(list("spat_point_alpha")), list("transparancy of spatial points")), "\n", " ", list(list(list("spat_point_border_col")), list("border color of spatial points")), "\n",
" ", list(list(list("spat_point_border_stroke")), list("border stroke of spatial points")), "\n", " ", list(list(list("dim_show_cluster_center")), list("show the center of each cluster")), "\n", " ", list(list(list("dim_show_center_label")), list("provide a label for each cluster")), "\n", " ", list(list(list("dim_center_point_size")), list("size of the center point")), "\n", " ", list(list(list("dim_center_point_border_col")), list("border color of center point")), "\n", " ",
list(list(list("dim_center_point_border_stroke")), list("stroke size of center point")), "\n", " ", list(list(list("dim_label_size")), list("size of the center label")), "\n", " ", list(list(list("dim_label_fontface")), list("font of the center label")), "\n", " ", list(list(list("spat_show_cluster_center")), list("show the center of each cluster")), "\n", " ", list(list(list("spat_show_center_label")), list("provide a label for each cluster")), "\n", " ", list(list(list("spat_center_point_size")),
list("size of the spatial center points")), "\n", " ", list(list(list("spat_center_point_border_col")), list("border color of the spatial center points")), "\n", " ", list(list(list("spat_center_point_border_stroke")), list("stroke size of the spatial center points")), "\n", " ", list(list(list("spat_label_size")), list("size of the center label")), "\n", " ", list(list(list("spat_label_fontface")), list("font of the center label")), "\n", " ", list(list(list("show_NN_network")),
list("show underlying NN network")), "\n", " ", list(list(list("nn_network_to_use")), list("type of NN network to use (kNN vs sNN)")), "\n", " ", list(list(list("nn_network_name")), list("name of NN network to use, if show_NN_network = TRUE")), "\n", " ", list(list(list("dim_edge_alpha")), list("column to use for alpha of the edges")), "\n", " ", list(list(list("spat_show_network")), list("show spatial network")), "\n", " ", list(list(list("spatial_network_name")), list("name of spatial network to use")),
"\n", " ", list(list(list("spat_network_color")), list("color of spatial network")), "\n", " ", list(list(list("spat_network_alpha")), list("alpha of spatial network")), "\n", " ", list(list(list("spat_show_grid")), list("show spatial grid")), "\n", " ", list(list(list("spatial_grid_name")), list("name of spatial grid to use")), "\n", " ", list(list(list("spat_grid_color")), list("color of spatial grid")), "\n", " ", list(list(list("show_other_cells")), list("display not selected cells")),
"\n", " ", list(list(list("other_cell_color")), list("color of not selected cells")), "\n", " ", list(list(list("dim_other_point_size")), list("size of not selected dim cells")), "\n", " ", list(list(list("spat_other_point_size")), list("size of not selected spat cells")), "\n", " ", list(list(list("spat_other_cells_alpha")), list("alpha of not selected spat cells")), "\n", " ", list(list(list("coord_fix_ratio")), list("ratio for coordinates")), "\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("legend_symbol_size")), list(
"size of legend symbols")), "\n", " ", list(list(list("dim_background_color")), list("background color of points in dim. reduction space")), "\n", " ", list(list(list("spat_background_color")), list("background color of spatial points")), "\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 plot")), "\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¶
- Other spatial and dimension reduction cell annotation visualizations:
``spatDimCellPlot2D` <#spatdimcellplot2d>`_
Examples¶
data(mini_giotto_single_cell)
# combine all metadata
combineMetadata(mini_giotto_single_cell, spat_enr_names = 'cluster_metagene')
# visualize total expression information
spatDimCellPlot(mini_giotto_single_cell, cell_annotation_values = 'total_expr')
# visualize enrichment results
spatDimCellPlot(mini_giotto_single_cell,
spat_enr_names = 'cluster_metagene',
cell_annotation_values = c('1','2'))