dimGenePlot2D

Visualize gene expression according to dimension reduction coordinates

dimGenePlot2D(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  genes = NULL,
  dim_reduction_to_use = "umap",
  dim_reduction_name = "umap",
  dim1_to_use = 1,
  dim2_to_use = 2,
  show_NN_network = F,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  network_color = "lightgray",
  edge_alpha = NULL,
  scale_alpha_with_expression = FALSE,
  point_shape = c("border", "no_border"),
  point_size = 1,
  point_alpha = 1,
  cell_color_gradient = c("blue", "white", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  point_border_col = "black",
  point_border_stroke = 0.1,
  show_legend = T,
  legend_text = 8,
  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 = "dimGenePlot2D"
)

Arguments

gobject

giotto object

expression_values

gene expression values to use

genes

genes to show

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

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

network_color

color of NN network

edge_alpha

column to use for alpha of the edges

scale_alpha_with_expression

scale expression with ggplot alpha parameter

point_shape

point with border or not (border or no_border)

point_size

size of point (cell)

point_alpha

transparancy of points

cell_color_gradient

vector with 3 colors for numeric data

gradient_midpoint

midpoint for color gradient

gradient_limits

vector with lower and upper limits

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

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 plots

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.

See also

dimGenePlot3D

Other dimension reduction gene expression visualizations: dimGenePlot3D(), dimGenePlot()

Examples

data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1:2]
dimGenePlot2D(mini_giotto_single_cell, genes = selected_genes, point_size = 3)