plotFCPseudocolor {TCC} | R Documentation |
This function creates a pseudo-color image of simulation data regarding the number of differentially expressed genes (DEGs) and the breakdowns for individual groups from a TCC-class object.
plotFCPseudocolor(tcc, main, xlab, ylab)
tcc |
TCC-class object. |
main |
character string indicating the plotting title. |
xlab |
character string indicating the x-label title. |
ylab |
character string indicating the y-label title. |
This function should be used after the
simulateReadCounts
function that generates
simulation data with arbitrary defined conditions.
The largest log fold-change (FC) values are
in magenta and no-changes are in white.
# Generating a simulation data for comparing two groups # (G1 vs. G2) with biological replicates. # the first 200 genes are DEGs, where 180 are up in G1. tcc <- simulateReadCounts(Ngene = 1000, PDEG = 0.2, DEG.assign = c(0.9, 0.1), DEG.foldchange = c(4, 4), replicates = c(3, 3)) plotFCPseudocolor(tcc) # Generating a simulation data for comparing three groups # (G1 vs. G2 vs. G3) with biological replicates. # the first 300 genes are DEGs, where the 70%, 20%, and 10% are # up-regulated in G1, G2, G3, respectively. The levels of DE are # 3-, 10, and 6-fold in individual groups. tcc <- simulateReadCounts(Ngene = 1000, PDEG = 0.3, DEG.assign = c(0.7, 0.2, 0.1), DEG.foldchange = c(3, 10, 6), replicates = c(3, 3, 3)) plotFCPseudocolor(tcc)