dimPlot2D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_visuals.R#L1137

Description#

Visualize cells according to dimension reduction coordinates

Usage#

dimPlot2D(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  group_by = NULL,
  group_by_subset = NULL,
  dim_reduction_to_use = "umap",
  dim_reduction_name = NULL,
  dim1_to_use = 1,
  dim2_to_use = 2,
  spat_enr_names = NULL,
  show_NN_network = FALSE,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  cell_color = NULL,
  color_as_factor = TRUE,
  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 = TRUE,
  other_cell_color = "lightgrey",
  other_point_size = 0.5,
  show_cluster_center = FALSE,
  show_center_label = TRUE,
  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 = TRUE,
  legend_text = 10,
  legend_symbol_size = 2,
  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#

Argument

Description

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 `showSaveP arameters <#showsaveparameters>`__

default_save_name

default save name for saving, don’t change, change save_name in save_param

Details#

Description of parameters. For 3D plots see `dimPlot3D <#dimplot3d>`__

Value#

ggplot

Seealso#

Other reduced dimension visualizations: `dimPlot3D <#dimplot3d>`__ , `dimPlot <#dimplot>`__ , `plotPCA_2D <#plotpca2d>`__ , `plotPCA_3D <#plotpca3d>`__ , `plotPCA <#plotpca>`__ , `plotTSNE_2D <#plottsne2d>`__ , `plotTSNE_3D <#plottsne3d>`__ , `plotTSNE <#plottsne>`__ , `plotUMAP_2D <#plotumap2d>`__ , `plotUMAP_3D <#plotumap3d>`__ , `plotUMAP <#plotumap>`__