View source: R/FateID_functions.R
plotdiffgenesnb | R Documentation |
This is a plotting function for visualizing the output of the diffexpnb
function as MA plot.
plotdiffgenesnb( x, pthr = 0.05, padj = TRUE, lthr = 0, mthr = -Inf, Aname = NULL, Bname = NULL, show_names = TRUE, ... )
x |
output of the function |
pthr |
real number between 0 and 1. This number represents the p-value cutoff applied for displaying differentially expressed genes. Default value is 0.05. The parameter |
padj |
logical value. If |
lthr |
real number between 0 and Inf. Differentially expressed genes are displayed only for log2 fold-changes greater than |
mthr |
real number between -Inf and Inf. Differentially expressed genes are displayed only for log2 mean expression greater than |
Aname |
name of expression set |
Bname |
name of expression set |
show_names |
logical value. If |
... |
Additional arguments for function |
None
x <- intestine$x y <- intestine$y v <- intestine$v tar <- c(6,9,13) fb <- fateBias(x,y,tar,z=NULL,minnr=5,minnrh=10,nbfactor=5,use.dist=FALSE,seed=NULL,nbtree=NULL) thr <- .3 A <- rownames(fb$probs)[fb$probs[,"t6"] > .3] B <- rownames(fb$probs)[fb$probs[,"t13"] > .3] de <- diffexpnb(v,A=A,B=B) plotdiffgenesnb(de,pthr=.05)
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