gating_tree_plot: Plot gating tree as a graph to explore how populations are...

In Close-your-eyes/fcexpr: Complement the manual analysis of flow cytometric experiments and organize your fcs files in a consistent way

Plot gating tree as a graph to explore how populations are gated in a simple way

Description

Plot gating tree as a graph to explore how populations are gated in a simple way

Usage

gating_tree_plot(
  PopulationFullPath,
  layout = "tree",
  find_short_gating_path = T,
  ...
)

Arguments

PopulationFullPath	vector of all populations path (full) gated in a (flowjo) workspace; optionally provide named vector (e.g. with short names) which will be plotted in the graph at correponding nodes
layout	layout for plotting, see ?ggraph::ggraph or ?ggraph::layout_tbl_graph_igraph
find_short_gating_path	if PopulationFullPath is a vector without names find the shortest unique gating path from these full paths for plotting
...	additional argument to ggrepel, like max.overlaps

Value

list of plot, graph and data.frame

Examples

## Not run: 
# Get count data frame from flowjo wsp
ps_counts <- fcexpr::wsx_get_popstats(ws = ws)[["counts"]]
# check if gatingtree is unique
dplyr::group_by(ps_counts, PopulationFullPath) %>% dplyr::count()
# generate graph
graph_list <- fcexpr::gating_tree_plot(PopulationFullPath = unique(ps_counts$PopulationFullPath))
# manual plotting graph to modify (e.g. layout)
plot <- ggraph::ggraph(graph_list[["graph"]], layout = "tree") +
ggraph::geom_edge_link() +
ggraph::geom_node_point(size = 4) +
ggraph::geom_node_label(ggplot2::aes(label = Population), repel = T)

## color nodes by a lineage marker
igraph::V(graph_list[["graph"]])$subname <- dplyr::case_when(grepl("CD3\\+", igraph::V(graph_list[["graph"]])$name) &
                                                         !grepl("CD8\\+|CD4\\+", igraph::V(graph_list[["graph"]])$name) ~ "CD3+",
                                                         grepl("CD8\\+", igraph::V(graph_list[["graph"]])$name) ~ "CD8+",
                                                         grepl("CD4\\+", igraph::V(graph_list[["graph"]])$name) ~ "CD4+",
                                                         grepl("CD19\\+", igraph::V(graph_list[["graph"]])$name) ~ "CD19+",
                                                         grepl("CD66b\\+", igraph::V(graph_list[["graph"]])$name) ~ "CD66b+",
                                                         grepl("CD11c\\+", igraph::V(graph_list[["graph"]])$name) ~ "CD11c+",
                                                         grepl("CD56\\+|NK", igraph::V(graph_list[["graph"]])$name) ~ "NK")

## End(Not run)

Close-your-eyes/fcexpr documentation built on Sept. 29, 2023, 12:27 a.m.