plotBar_MCI: plot MCI barplots

In xyang2uchicago/NPS: BioTIP: An R package for characterization of Biological Tipping-Point

plot MCI barplots

Description

A barplot of MCI for all clusters in all states.

Usage

plotBar_MCI(
  MCIl,
  ylim = NULL,
  nr = 1,
  nc = NULL,
  order = NULL,
  minsize = 3,
  states = NULL
)

Arguments

MCIl	A list can be obtained through getMCI.
ylim	A vector needed if the output barplots need to be on the same y scale.
nr	The number of rows to plot.
nc	The number of columns to plot, default length(groups).
order	A character vector of the order of the barplot. Default is NULL which uses the input list order.
minsize	A non-negative numeric value of minimum size allowed for a cluster.
states	A character of the state names to be shown on the plot. Default is NULL, assign this if you want to show all states including states without nodes.

Value

Return a barplot of MCI scores across states.

Author(s)

Zhezhen Wang [e-mail]

References

Chen L, Liu R, Liu Z, Li M & Aihara K (2012) Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers Scientific Reports 2:342

Examples

test = list('state1' = matrix(sample(1:10, 6), 4, 3), 
  'state2' = matrix(sample(1:10, 6), 4, 3), 
  'state3' = matrix(sample(1:10, 6), 4, 3))
# assign colnames and rownames to the matrix
for(i in names(test)){
 colnames(test[[i]]) = 1:3
 row.names(test[[i]]) = c('g1', 'g2', 'g3', 'g4')
}

cluster = list(c(1, 2, 2, 1),  c(1, 2, 3, 1),  c(2, 2, 1, 1))
names(cluster) = names(test)
for(i in names(cluster)){
 names(cluster[[i]]) = c('g1', 'g2', 'g3', 'g4')
}
membersL_noweight <- getMCI(cluster, test)
plotBar_MCI(membersL_noweight)

xyang2uchicago/NPS documentation built on June 30, 2024, 10:15 p.m.