plotUMAP

Short wrapper for UMAP visualization

Usage

plotUMAP(gobject, dim_reduction_name = NULL, 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

spat_unit: spatial unit (e.g. "cell")
feat_type: feature type (e.g. "rna", "dna", "protein")
show_plot: logical. show plot
return_plot: logical. return ggplot object
save_plot: logical. save the plot
save_param: list of saving parameters, see showSaveParameters
dim1_to_use: numeric. dimension to use on x-axis
dim2_to_use: numeric. dimension to use on y-axis
show_NN_network: logical. Show underlying NN network
nn_network_to_use: character. type of NN network to use (kNN vs sNN)
network_name: character. name of NN network to use, if show_NN_network = TRUE
spat_enr_names: character. names of spatial enrichment results to include
cell_color: character. what to color cells by (e.g. metadata col or spatial enrichment col)
color_as_factor: logical. convert color column to factor. Discrete colors are used when this is TRUE. continuous colors when FALSE.
cell_color_code: character. discrete colors to use. palette to use or named vector of colors
cell_color_gradient: character. continuous colors to use. palette to use or vector of colors to use (minimum of 2).
cow_n_col: cowplot param: how many columns
cow_rel_h: cowplot param: relative heights of rows (e.g. c(1,2))
cow_rel_w: cowplot param: relative widths of columns (e.g. c(1,2))
cow_align: cowplot param: how to align
group_by: character. Create multiple plots based on cell annotation column
group_by_subset: character. subset the group_by factor column
gradient_midpoint: numeric. midpoint for color gradient
gradient_style: either 'divergent' (midpoint is used in color scaling) or 'sequential' (scaled based on data range)
gradient_limits: numeric 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 for not selected cells
other_point_size: point size for 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 points
point_border_col: color of border around points
point_border_stroke: stroke size of border around points
title: character. title for plot, defaults to cell_color parameter
show_legend: logical. 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

Value

ggplot

Examples

g <- GiottoData::loadGiottoMini("visium", verbose = FALSE)
#> 
#> 1. use installGiottoEnvironment() to install
#>  a local miniconda python environment along with required modules
#> 
#> 2. provide an existing python path to
#>  python_path to use your own python path which has all modules
#>  installed
#> Set options("giotto.use_conda" = FALSE) if
#>  python functionalities are not needed
plotUMAP(g)

Usage

Arguments

Value

See also

Examples