RankView {MAGeCKFlute} | R Documentation |
Rank all genes according to beta score deviation, and label top and bottom meaningful genes. Some other interested genes can be labeled too.
RankView(rankdata, genelist = c(), top = 20, bottom = 20, cutoff = c(-sd(rankdata), sd(rankdata)), main = NULL, filename = NULL, width = 5, height = 4, ...)
rankdata |
Numeric vector, with gene as names. |
genelist |
Character vector, specifying genes to be labeled in figure. |
top |
Integer, specifying number of top genes to be labeled. |
bottom |
Integer, specifying number of bottom genes to be labeled. |
cutoff |
A two-length numeric vector, in which first value is bottom cutoff, and second value is top cutoff. |
main |
As in 'plot'. |
filename |
Figure file name to create on disk. Default filename="NULL", which means no output. |
width |
As in ggsave. |
height |
As in ggsave. |
... |
Other available parameters in function 'ggsave'. |
An object created by ggplot
, which can be assigned and further customized.
Wubing Zhang
data(MLE_Data) # Read beta score from gene summary table in MAGeCK MLE results dd = ReadBeta(MLE_Data, organism="hsa") rankdata = dd$PLX7_R1 - dd$D7_R1 names(rankdata) = rownames(dd) RankView(rankdata)