plotClusterGraph: Plot cluster graph generated with makeClusterGraph.

Description Usage Arguments

View source: R/graph_visualization.R

Description

In this visualization, edges are colored in black when AUROC > 0.5 and orange when AUROC < 0.5, edge width scales linearly with AUROC. Edges are oriented from training cluster towards test cluster. A black bidirectional edge indicates that two clusters are reciprocal top matches. Node radius reflects cluster size (small: up to 10 cells, medium: up to 100 cells, large: all other clusters).

Usage

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plotClusterGraph(
  graph,
  study_id = NULL,
  cell_type = NULL,
  size_factor = 1,
  label_cex = 0.2 * size_factor,
  legend_cex = 2,
  study_cols = NULL
)

Arguments

graph

Graph in igraph format generated by makeClusterGraph.

study_id

Vector with study IDs provided to MetaNeighborUS to compute AUROCs stored in graph (used to compute cluster size). If NULL, all nodes have medium size.

cell_type

Vector with cell type labels provided to MetaNeighborUS to compute AUROCs stored in graph (used to compute cluster size). If NULL, all nodes have medium size.

size_factor

Numeric value controling the size of nodes and edges.

label_cex

Numeric value controling the size of cell type labels.

legend_cex

Numeric value controling the size of the legend.

study_cols

Named vector where values are RGB colors and names are unique study identifiers. If NULL, a default color palette is used.


MetaNeighbor documentation built on Nov. 8, 2020, 5:40 p.m.