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Plot multiple markers on multiple graphs

Plot2DGraphM.Rd

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.

Usage

Plot2DGraphM(
  object,
  cells,
  markers,
  assay = NULL,
  layout_method = c("pmds", "wpmds", "fr", "kk", "drl"),
  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 = FALSE,
  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?

log_scale

Convert node counts to log-scale with log1p

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 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

See also

Plot2DGraph()

Examples

library(pixelatorR)

pxl_file <- system.file("extdata/five_cells",
  "five_cells.pxl",
  package = "pixelatorR"
)

seur <- ReadMPX_Seurat(pxl_file)
#> ✔ Created a 'Seurat' object with 5 cells and 80 targeted surface proteins
seur <- LoadCellGraphs(seur, load_as = "Anode")
#> →    Loading CellGraphs for 5 cells from sample 1
#> ✔ Successfully loaded 5 CellGraph object(s).
seur <- ComputeLayout(seur, layout_method = "pmds", dim = 2)
#> ℹ Computing layouts for 5 graphs

Plot2DGraphM(seur, cells = colnames(seur)[2:3], markers = c("CD20", "CD4"))
#> ✖ 'CD20' is missing from node count matrix for component RCVCMP0000487