gene2gene {FateID} | R Documentation |
Comparative plot of the expression levels of two genes
Description
This function produces a scatter plot of the expression levels of two genes. It allows plotting cells of selected clusters and permits highlighting of the fate bias.
Usage
gene2gene(
x,
y,
g1,
g2,
clusters = NULL,
fb = NULL,
tn = NULL,
col = NULL,
tp = 1,
plotnum = TRUE,
seed = 12345
)
Arguments
x |
expression data frame with genes as rows and cells as columns. Gene IDs should be given as row names and cell IDs should be given as column names. This can be a reduced expression table only including the features (genes) to be used in the analysis. |
y |
clustering partition. A vector with an integer cluster number for each cell. The order of the cells has to be the same as for the columns of x. |
g1 |
gene id corresponding to a valid row names of x. Expression of gene |
g2 |
gene id corresponding to a valid row names of x. Expression of gene |
clusters |
vector of valid cluster ids. Expression is displayed for cells in any of the clusters contained in |
fb |
fateBias object returned by the function |
tn |
name of a target cluster, i. e. concatenation of a |
col |
optional vector of valid color names for all clusters in |
tp |
Transparency of points in the plot. Default value is 1, i. e. non-transparent. |
plotnum |
logical value. If |
seed |
integer number. Random seed for determining colour scheme. Default is 12345. |
Value
None
Examples
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)
gene2gene(v,y,"Muc2__chr7","Apoa1__chr9")
gene2gene(v,y,"Muc2__chr7","Apoa1__chr9",fb=fb,tn="t6",plotnum=FALSE)