xina_plot_all: xina_plot_all

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

Description

xina_plot_all is to draw protein-protein interaction network plots of all the clusters

Usage

xina_plot_all(xina_result, clustering_result, condition = "all",
  centrality_type = NULL, flag_simplify = TRUE, num_breaks = 5,
  layout_specified = "", vertex_label_flag = FALSE,
  vertex.label.color = "black", vertex.color = "", edge.color = NULL,
  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_clusters_in_row = 5,
  flag_unknown_only = FALSE, img_size = NULL, img_qual = 300)

Arguments

xina_result	A list containing XINA network analysis results. See xina_analysis
clustering_result	A list containing XINA clustering results. See xina_clustering
condition	Default is 'all', which means use all the proteins to draw graphs. If you specify the experimental condition name used for XINA clustering, xina_plot_all will draw graphs using specific condition's proteins.
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
num_breaks	'num_breaks' is the number of ranks based on network centrality. Default is 5.
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.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 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'.
num_clusters_in_row	The number of clusters in a row on the XINA network plot. Default is 5.
flag_unknown_only	If this is TRUE, 'xina_plot_all' will plot proteins that do not have any protein-protein interaction in the given database
img_size	Set the image size. For width=1000 and height=1500, it is img_size=c(1000,1500). Default is c(3000,3000)
img_qual	Set the image resolution. Default is 300.

Value

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)

# XINA network plots
xina_plot_all(xina_result_example, example_clusters)

# XINA network plots for Control condition
xina_plot_all(xina_result_example, example_clusters, condition='Control')

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