dimGenePlot2D: dimGenePlot2D
In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

dimGenePlot2D

R Documentation

dimGenePlot2D

Description

Visualize gene expression according to dimension reduction coordinates

Usage

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

Details

Description of parameters.

Value

ggplot

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)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.