Visualize Cells By Coordinates¶

dimPlot2D()

Visualize cells according to dimension reduction coordinates.

dimPlot2D(
    gobject,
    group_by = NULL,
    group_by_subset = NULL,
    dim_reduction_to_use = "umap",
    dim_reduction_name = "umap",
    dim1_to_use = 1,
    dim2_to_use = 2,
    spat_enr_names = NULL,
    show_NN_network = F,
    nn_network_to_use = "sNN",
    network_name = "sNN.pca",
    cell_color = NULL,
    color_as_factor = T,
    cell_color_code = NULL,
    cell_color_gradient = c("blue", "white", "red"),
    gradient_midpoint = NULL,
    gradient_limits = NULL,
    select_cell_groups = NULL,
    select_cells = NULL,
    show_other_cells = T,
    other_cell_color = "lightgrey",
    other_point_size = 0.5,
    show_cluster_center = F,
    show_center_label = T,
    center_point_size = 4,
    center_point_border_col = "black",
    center_point_border_stroke = 0.1,
    label_size = 4,
    label_fontface = "bold",
    edge_alpha = NULL,
    point_shape = c("border", "no_border"),
    point_size = 1,
    point_alpha = 1,
    point_border_col = "black",
    point_border_stroke = 0.1,
    title = NULL,
    show_legend = T,
    legend_text = 8,
    legend_symbol_size = 1,
    background_color = "white",
    axis_text = 8,
    axis_title = 8,
    cow_n_col = 2,
    cow_rel_h = 1,
    cow_rel_w = 1,
    cow_align = "h",
    show_plot = NA,
    return_plot = NA,
    save_plot = NA,
    save_param = list(),
    default_save_name = "dimPlot2D"
)

Arguments¶

gobject	giotto object
group_by	create multiple plots based on cell annotation column
group_by_subset	subset the group_by factor column
dim_reduction_to_use	dimension reduction to use
dim_reduction_name	dimension reduction name
dim1_to_use	dimension to use on x-axis
dim2_to_use	dimension to use on y-axis
spat_enr_names	names of spatial enrichment results to include
show_NN_network	show underlying NN network
nn_network_to_use	type of NN network to use (kNN vs sNN)
network_name	name of NN network to use, if show_NN_network = TRUE
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
show_other_cells	display not selected cells
other_cell_color	color of not selected cells
other_point_size	size of not selected cells
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
edge_alpha	column to use for alpha of the edges
point_shape	point with border or not (border or no_border)
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
title	title for plot, defaults to cell_color parameter
show_legend	show legend
legend_text	size of legend text
legend_symbol_size	size of legend symbols
background_color	color of plot background
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`

Value¶

A ggplot.

Details¶

Description of parameters …

See dimPlot2D() and dimPlot3D() for 3D plot information.

Examples¶

data(mini_giotto_single_cell)
dimPlot2D(mini_giotto_single_cell)

dimPlot(mini_giotto_single_cell, cell_color = 'cell_types', point_size = 3)