xina_plot_single: xina_plot_single

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

Description

xina_plot_single draws protein-protein interaction network plot for given 'protein_list'.

Usage

xina_plot_single(xina_result, protein_list, centrality_type = NULL,
  layout_specified = "", vertex_label_flag = TRUE, main = NULL,
  vertex.label.color = "black", vertex.color = NA,
  edge.color = "darkgray", vertex.label.dist = 0.6,
  vertex.label.cex = 0.8, edge.arrow.size = 0.4, vertex.size = 10,
  vertex.shape = "sphere", legend_location = "bottom",
  num_breaks = 5, digits_round_up = 5, flag_simplify = TRUE,
  flag_legend = TRUE)

Arguments

xina_result	A list containing XINA network analysis results. See xina_analysis
protein_list	A vector of gene names to draw a protein-protein interaction network graph.
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
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
main	Title of network figure. IF it is NULL (default), it will be the number of plotted proteins
vertex.label.color	Color of labels. Default is black
vertex.color	Color of nodes. Default is pink.
edge.color	Color of edges. Default is pink.
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
legend_location	If centrality_type is chosen, 'xina_plot_single' adds 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'.
num_breaks	'num_breaks' is the number of ranks based on network centrality. Default is 5.
digits_round_up	See Round
flag_simplify	If it is TRUE (default), XINA will exclude unconnected proteins
flag_legend	If it is TRUE, a legend will be printed out together.

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

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)

# get gene names that are clustered to #21 in "Stimulus2" condition
subgroup <- subset(example_clusters$aligned, Stimulus2==21)
protein_list <- subgroup$`Gene name`

# Calculate protein-protein interaction network
xina_plot_single(xina_result_example, protein_list)

# Calculate protein-protein interaction network and Eigenvector centrality
eigen_info <- xina_plot_single(xina_result_example, protein_list, centrality_type='Eigenvector')

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