Plot dimension reduction

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 = NULL,
  gradient_midpoint = NULL,
  gradient_style = c("divergent", "sequential"),
  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 = NULL,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h",
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "dimPlot2D"
)

dimPlot(...)

dimPlot3D(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  dim_reduction_to_use = "umap",
  dim_reduction_name = "umap",
  dim1_to_use = 1,
  dim2_to_use = 2,
  dim3_to_use = 3,
  spat_enr_names = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  show_other_cells = TRUE,
  other_cell_color = "lightgrey",
  other_point_size = 2,
  show_NN_network = FALSE,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  color_as_factor = TRUE,
  cell_color = NULL,
  cell_color_code = NULL,
  show_cluster_center = FALSE,
  show_center_label = TRUE,
  center_point_size = 4,
  label_size = 4,
  edge_alpha = NULL,
  point_size = 3,
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "dim3D"
)

Arguments

gobject: giotto object
spat_unit: spatial unit (e.g. "cell")
feat_type: feature type (e.g. "rna", "dna", "protein")
group_by: character. Create multiple plots based on cell annotation column
group_by_subset: character. subset the group_by factor column
dim_reduction_to_use: character. dimension reduction to use
dim_reduction_name: character. dimension reduction name
dim1_to_use: numeric. dimension to use on x-axis
dim2_to_use: numeric. dimension to use on y-axis
spat_enr_names: character. names of spatial enrichment results to include
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
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).
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
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: logical. show plot
return_plot: logical. return ggplot object
save_plot: logical. save the plot
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
...: dimPlot(...) passes to dimPlot2D()
dim3_to_use: numeric. dimension to use on z-axis

Value

ggplot

plotly (dimplot3D only)

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
dimPlot2D(g)

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
dimPlot(g)

Usage

Arguments

Value

See also

Examples