dimPlot#

Last Updated: May 20, 2025

Description#

Visualize cells according to dimension reduction coordinates

Usage#

dimPlot(...)

Arguments#

...

Arguments passed on to dimPlot2D

gobject: giotto object
spat_unit: spatial unit
feat_type: feature type
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 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
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

Details#

Description of parameters, see dimPlot2D. For 3D plots see dimPlot3D

Value#

ggplot