Description Usage Arguments Details Value Author(s) References See Also Examples
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.
1 2 3 4 | difconet.plot.histograms.heatmap2(dObj,
genes=1:10,
stages=1:length(dObj$stages.data),
qprobs=c(0,.50,.975,.995), ...)
|
dObj |
The difconet object. |
genes |
Numeric or character. The gene indexes/rownames included. |
stages |
Numeric or character. The stages to be included. |
qprobs |
The quantiles used to draw the heatmap. Should be 4 points. Each has specific color codes. |
... |
Further parameters passed to plot/pairs. |
A heatmap is draw representing the distribution of correlations of several genes across stages.
Nothing.
Elpidio Gonzalez and Victor Trevino vtrevino@itesm.mx
Gonzalez-Valbuena and Trevino 2017 Metrics to Estimate Differential Co-Expression Networks Journal Pending volume 00–10
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | xdata <- matrix(rnorm(1000), ncol=100)
xpredictor <- sample(c("A","B","C","D"),100,replace=TRUE)
dObj <- difconet.run(xdata, xpredictor, metric = 4, num_perms = 10,
comparisons = list(c("A","D"), c("A","B"), c("B","D")),
perm_mode = "columns")
#Top highest metric in first comparison but showing correlations in only 3 stages
difconet.plot.gene.correlations(dObj, order(dObj$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")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.