Description Usage Arguments Details Value Author(s) References See Also Examples
Draw scatter plots of the correlations of a specific gene.
1 2 3 4 |
dObj |
The difconet object. |
gene |
Numeric or character. The gene index/rowname whose correlations will be drawn. |
stages |
Numeric or character. The stages to be included. If type="scatter" and more than two stages, a call to pairs is used instead of plot. |
type |
Character. The type of plot density or scatter. |
main |
Character. The main title passed to plot. |
legends |
Logical. Specifies whether the legends are drawn when type="density". |
plot |
Logical. Specifies whether the plots are actually drawn (to get the correlations). |
... |
Further parameters passed to plot/pairs. |
Run the whole process of estimation differences in correlations for a given dataset. The estimations are done for all metric values, all cutoff values across all comparisons.
The correlations of the gene across stages (invisible).
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 (3), showing densities of correlations
difconet.plot.gene.correlations(dObj, 3, type="d")
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