`dimCellPlot`¶

dimCellPlot

Description¶

Visualize cells according to dimension reduction coordinates

Usage¶

dimCellPlot(gobject, ...)

Arguments¶

Argument

Description

gobject

giotto object

...

Arguments passed on to ``dimCellPlot2D` <#dimcellplot2d>`_ list(“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(“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("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("network_name")), list("name of NN network to use, if show_NN_network = TRUE")), "\n", "    ", list(list(list("cell_color_code")), list("named vector with colors for cell annotation values")), "\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("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("other_point_size")), list("size of not selected cells")), "\n", "    ", list(list(list("show_cluster_center")), list("plot center of selected clusters")), "\n", "    ", list(list(list("show_center_label")), list("plot label of selected clusters")), "\n", "    ", list(list(list("center_point_size")), list("size of center points")), "\n", "    ",
list(list(list("center_point_border_col")), list("border color of center points")), "\n", "    ", list(list(list("center_point_border_stroke")), list("border stroke size of center points")), "\n", "    ", list(list(list("label_size")), list("size of labels")), "\n", "    ", list(list(list("label_fontface")), list("font of labels")), "\n", "    ", list(list(list("edge_alpha")), list("column to use for alpha of the edges")), "\n", "    ", list(list(list("point_shape")), list("point with border or not (border or no_border)")),
"\n", "    ", list(list(list("point_size")), list("size of point (cell)")), "\n", "    ", list(list(list("point_alpha")), list("transparancy of dim. reduction 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("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("background_color")), list("color of plot background")), "\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("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_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. For 3D plots see ``dimCellPlot2D` <#dimcellplot2d>`_

Value¶

ggplot

Seealso¶

Other dimension reduction cell annotation visualizations:: ``dimCellPlot2D` <#dimcellplot2d>`_

Examples¶

data(mini_giotto_single_cell)

# combine all metadata
combineMetadata(mini_giotto_single_cell, spat_enr_names = 'cluster_metagene')

# visualize total expression information
dimCellPlot(mini_giotto_single_cell, cell_annotation_values = 'total_expr')

# visualize enrichment results
dimCellPlot(mini_giotto_single_cell,
spat_enr_names = 'cluster_metagene',
cell_annotation_values = c('1','2'))

dimCellPlot¶