xina_plot_bycluster: xina_plot_bycluster

In langholee/XINA: Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

Description

xina_plot_bycluster is to draw protein-protein interaction network plots of each cluster

Usage

xina_plot_bycluster(xina_result, clustering_result, cl = NULL,
  condition = "all", flag_legend = TRUE, centrality_type = NULL,
  flag_simplify = TRUE, layout_specified = "",
  vertex_label_flag = TRUE, vertex.label.dist = 0.6,
  vertex.label.cex = 0.8, edge.arrow.size = 0.4, vertex.size = 10,
  vertex.shape = "sphere", vertex.color = "",
  edge.color = "darkgray", legend_location = "bottom",
  flag_unknown_only = FALSE)

Arguments

xina_result	A list containing XINA network analysis results. See xina_analysis
clustering_result	A list containing XINA clustering results. See xina_clustering
cl	Cluster number in the XINA clustering results
condition	Default is 'all', which means use all the proteins to draw graphs. If you specify the experimental condition name used for XINA clustering,
flag_legend	If it is TRUE, a legend will be printed out together.
centrality_type	'centrality_type' should be one of c('Degree', 'Eigenvector', 'Hub', 'Authority', 'Closeness', 'Betweenness') Centrality score igraph function Degree degree Eigenvector eigen_centrality Hub hub_score Authority authority_score Closeness closeness Betweenness betweenness
flag_simplify	If it is TRUE (default), XINA will exclude unconnected proteins
layout_specified	This can change network layout. 'layout_specified' should be one of c('sphere', 'star', 'gem', 'tree', 'circle', 'random', 'nicely'). XINA's layouts are based on igraph's layout. See layout_ Layout igraph layout name sphere layout_on_sphere star layout_as_star gem layout_with_gem tree layout_as_tree circle layout_in_circle random layout_randomly nicely layout_nicely Default is 'layout_nicely' of igraph
vertex_label_flag	If vertex_label_flag is TRUE (default), igraph network graphs will be labeled by gene names If vertex_label_flag is FALSE, igraph network graphs will be drawn without labels
vertex.label.dist	Distance between node and label. Default is 0.6
vertex.label.cex	Size of labels Default is 0.8
edge.arrow.size	Size of edges Default is 0.4
vertex.size	Size of nodes Default is 10
vertex.shape	You can choose node shape. Default is 'sphere'. See shapes
vertex.color	Color of nodes. Default is pink.
edge.color	Color of edges. Default is pink.
legend_location	If centrality_type is chosen, xina_plot_single add the color legend guiding rank of nodes based on the centrality score. Default is 'bottomright', but you can choose one of these 'bottomright', 'bottom', 'bottomleft', 'left', 'topleft', 'top', 'topright', 'right' and 'center'.
flag_unknown_only	If this is TRUE, 'xina_plot_bycluster' will plot proteins that do not have any protein-protein interaction in the given database

Value

A PNG file (XINA_Cluster_Networks.png) displaying protein-protein interaction network plots of all the clusters and a list containing XINA network analysis results

PNG images of PPI network plots of all the clusters

Examples

## the following code is to show how it works quickly
## load XINA example data
data(xina_example)

## load the previously processed XINA analysis results
# if you want to learn how to run 'xina_analysis', please see \link[XINA]{xina_analysis}
data(xina_result_example)

# plot cluster #1
xina_plot_bycluster(xina_result_example, example_clusters, cl=1)

# plot PPI network of Control condition in cluster #1
xina_plot_bycluster(xina_result_example, example_clusters, cl=1, condition='Control')

langholee/XINA documentation built on March 17, 2020, 5:23 p.m.