dimCellPlot2D

Visualize cells according to dimension reduction coordinates

dimCellPlot2D(
  gobject,
  dim_reduction_to_use = "umap",
  dim_reduction_name = "umap",
  dim1_to_use = 1,
  dim2_to_use = 2,
  spat_enr_names = NULL,
  cell_annotation_values = NULL,
  show_NN_network = F,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  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 = T,
  other_cell_color = "lightgrey",
  other_point_size = 0.5,
  show_cluster_center = F,
  show_center_label = T,
  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,
  show_legend = T,
  legend_text = 8,
  legend_symbol_size = 1,
  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 = "dimCellPlot2D"
)

Arguments

gobject: giotto object
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
cell_annotation_values: numeric cell annotation columns
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_code: named vector with colors for cell annotation values
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 dim. reduction points
point_border_col: color of border around points
point_border_stroke: stroke size of border around points
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 height
cow_rel_w: cowplot param: relative width
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

Value

ggplot

Details

Description of parameters. For 3D plots see dimPlot3D

Examples


data(mini_giotto_single_cell)

# combine all metadata
combineMetadata(mini_giotto_single_cell, spat_enr_names = 'cluster_metagene')

# visualize total expression information
dimCellPlot2D(mini_giotto_single_cell, cell_annotation_values = 'total_expr')

# visualize enrichment results
dimCellPlot2D(mini_giotto_single_cell,
               spat_enr_names = 'cluster_metagene',
               cell_annotation_values = c('1','2'))

Arguments

Value

Details

See also

Examples