UMAP Wrapper¶

plotUMAP()

Short wrapper for UMAP visualization.

plotUMAP(
    gobject,
    dim_reduction_name = "umap",
    default_save_name = "UMAP",
    ...
)

Arguments¶

gobject	giotto object
dim_reduction_name	name of UMAP
default_save_name	default save name of UMAP plot
…	Arguments passed on to dimPlot2D()
group_by	create multiple plots based on cell annotation column
group_by_subset	subset the group_by factor column
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	transparency 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()

Value¶

A ggplot.

Details¶

This is a wrapper function to generate a UMAP visualization from read depth normalized expression matrix.

UMAP can accept as input the original gene expression matrix (set dim_reduction_to_use=NULL) or the dimension reduced matrix from PCA (default) (dim_reduction_to_use=”pca”). If principle components are analyzed, then one specifies the dimensions_to_use.

It is possible to further define the number of neighbors (n_neighbors), number of epochs (n_epochs), and min_dist (see UMAP parameter guide here). The options set_seed and seed_number are helpful to fix the random number generation seed so that the same result is returned each time the function is run.

A plot will be returned in the result.

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

Examples¶

data(mini_giotto_single_cell)

plotUMAP(mini_giotto_single_cell)

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