difconet.plot.histograms.heatmap2 {difconet}

PLOT A HEATMAP REPRESENTATION OF THE DISTRIBUTION OF CORRELATIONS OF MANY GENES

Description

Draw a heatmap whose rows are genes and columns are segments of the histogram of the distribution of correlations per gene. The height/density of the histogram is shown in colors.

Usage

difconet.plot.histograms.heatmap2(dObj, 
  genes=1:10, 
  stages=1:length(dObj$stages.data), 
  qprobs=c(0,.50,.975,.995), ...)

Arguments

dObj

The difconet object.

genes

Numeric or character. The gene indexes/rownames included.

stages

Numeric or character. The stages to be included.

qprobs

The quantiles used to draw the heatmap. Should be 4 points. Each has specific color codes.

...

Further parameters passed to plot/pairs.

Details

A heatmap is draw representing the distribution of correlations of several genes across stages.

Value

Nothing.

Author(s)

Elpidio Gonzalez and Victor Trevino [e-mail]

References

Gonzalez-Valbuena and Trevino 2017 Metrics to Estimate Differential Co-Expression Networks Journal Pending volume 00–10

See Also

difconet.run.

Examples

xdata <- matrix(rnorm(1000), ncol=100)
xpredictor <- sample(c("A","B","C","D"),100,replace=TRUE)
dObj <- difconet.run(xdata, xpredictor, metric = 4, num_perms = 10,              
  comparisons = list(c("A","D"), c("A","B"), c("B","D")),
  perm_mode = "columns")

  #Top highest metric in first comparison but showing correlations in only 3 stages
  difconet.plot.gene.correlations(dObj, order(dObj$combstats[[1]][,"M4.dist"], 
    decreasing=TRUE)[1], type="s", stages=1:3)
  #Bottom lowest metric in second comparison showing all stages
  difconet.plot.gene.correlations(dObj, order(dObj$combstats[[2]][,"M4.dist"], 
    decreasing=TRUE)[1], type="d")
  #Another specific gene (1), showing densities of correlations
  difconet.plot.gene.correlations(dObj, 1, type="d")