xina_plot_single: xina_plot_single

Description Usage Arguments Value Examples

View source: R/network_plots.R

Description

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

Usage

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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

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## 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')

XINA documentation built on Nov. 8, 2020, 5:32 p.m.