plotBar_MCI {BioTIP} | R Documentation

## 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 zhezhen@uchicago.edu

### 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)

[Package BioTIP version 1.1.1 Index]