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Plot multiple markers on multiple graphs

Plot2DGraphM.Rd

[Deprecated]

Usage

Plot2DGraphM(
  object,
  cells,
  markers,
  assay = NULL,
  layout_method = c("cpmds_3d", "wpmds_3d", "pmds_3d", "cpmds", "wpmds", "pmds"),
  colors = c("lightgrey", "mistyrose", "red", "darkred"),
  map_nodes = TRUE,
  map_edges = FALSE,
  log_scale = TRUE,
  node_size = 0.5,
  edge_width = 0.3,
  show_Bnodes = TRUE,
  titles = NULL,
  titles_theme = NULL,
  titles_size = 10,
  titles_col = "black",
  ...
)

Arguments

object

A Seurat object

cells

A character vector with cell IDs

markers

A character vector with marker names

assay

Name of assay to pull data from

layout_method

Select appropriate layout previously computed with ComputeLayout

colors

A character vector of colors to color marker counts by

map_nodes, map_edges

Should nodes and/or edges be mapped? Note that component graphs can have >100k edges which can be very slow to draw.

log_scale

Convert node counts to log-scale with log1p. This parameter is ignored for PNA graphs.

node_size

Size of nodes

edge_width

Set the width of the edges if map_edges = TRUE

show_Bnodes

Should B nodes be included in the visualization? This option is only applicable to bipartite MPX graphs. Note that by removing the B nodes, all edges are removed from the graph and hence, map_edges will have no effect.

titles

A named character vector with optional titles. The names of titles should match cells

titles_theme

A theme used to style the titles

titles_size

The size of the text in the plot titles

titles_col

The color of the plot titles

...

Parameters passed to Plot2DGraph

Value

A patchwork object

Details

Deprecated. Use cell_plot() with cell_grid() instead.

In contrast to Plot2DGraph, which only draw 1 marker at the time, this function makes it possible to arrange plots into a grid with markers in rows and components in columns. The color scales are fixed for each marker so that their limits are the same across all components.

See also

cell_plot(), Plot2DGraph()

Examples

library(pixelatorR)

# Use cell_plot() with cell_grid() instead
if (FALSE) { # \dontrun{
# MPX
pxl_file <- minimal_mpx_pxl_file()
seur <- ReadMPX_Seurat(pxl_file)
seur <- LoadCellGraphs(seur, load_as = "Anode")
seur <- ComputeLayout(seur, layout_method = "cpmds", dim = 2)
Plot2DGraphM(seur, cells = colnames(seur)[2:3], layout_method = "cpmds", markers = c("CD20", "CD4"))

# PNA
pxl_file <- minimal_pna_pxl_file()
seur <- ReadPNA_Seurat(pxl_file)
seur <- LoadCellGraphs(seur, cells = colnames(seur)[2:3], add_layouts = TRUE)
seur <- ComputeLayout(seur, layout_method = "cpmds", dim = 2)
Plot2DGraphM(seur, cells = colnames(seur)[2:3], layout_method = "cpmds", markers = c("CD20", "CD4"))
} # }