plot_clusters: plot_clusters

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

Description

Draw all the clustering results. 'plot_clusters' draws two plots, scaled and unscaled line graphs. Scaled graphs have same y limits that are 0 to 1 by default, but can be changed via 'y_lim' parameter.

Usage

plot_clusters(clustering_result, y_lim = NULL, xval = NULL,
  xtickmark = NULL, xylab = TRUE, ggplot_theme = NULL)

Arguments

clustering_result	A list containing XINA clustering results. See xina_clustering
y_lim	Y axis limit. If you set y_lim=c(0,1), 'plot_clusters' will plot line graphs scaled from 0 to 1 in y-axis Default is NULL, which means unscaled line graphs.
xval	XINA basically considers time points as a ordinary variable, like 1,2,3,4...n. You can make the time points as a continuous variable using xval.
xtickmark	Change X axis tick marks. Default is data_column of the clustering result list.
xylab	If it is FALSE, x and y labels will be blank. If it is TRUE (defualt), x and y labels will be shown.
ggplot_theme	This is ggplot theme to modify XINA clustering plot.

Value

Line graphs of all the clusters

Examples

library(ggplot2)

# load XINA example data
data(xina_example)

# Draw clustering plots
plot_clusters(example_clusters)

# Apply theme to the clustering plot
theme1 <- theme(title=element_text(size=8, face='bold'),
axis.text.x = element_text(size=7),
axis.text.y = element_blank(),
axis.ticks.x = element_blank(),
axis.ticks.y = element_blank(),
axis.title.x = element_blank(),
axis.title.y = element_blank())
plot_clusters(example_clusters, ggplot_theme=theme1)

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