plotPCA

Short wrapper for PCA visualization

Usage

plotPCA(gobject, dim_reduction_name = NULL, default_save_name = "PCA", ...)

Arguments

gobject

giotto object

dim_reduction_name

name of PCA

default_save_name

default save name of PCA 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

Details

Description of parameters, see dimPlot2D. For 3D plots see plotPCA_3D

See also

Other reduced dimension visualizations: dimPlot2D(), plotPCA_2D(), plotPCA_3D(), plotTSNE(), plotTSNE_2D(), plotTSNE_3D(), plotUMAP(), plotUMAP_2D(), plotUMAP_3D()

Examples

g <- GiottoData::loadGiottoMini("visium", verbose = FALSE)
plotPCA(g)