plotSmoothers {tradeSeq} | R Documentation |
Plot the smoothers estimated by tradeSeq
.
plotSmoothers(models, ...) ## S4 method for signature 'gam' plotSmoothers( models, nPoints = 100, lwd = 2, size = 2/3, xlab = "Pseudotime", ylab = "Log(expression + 1)", border = TRUE, alpha = 1, sample = 1 ) ## S4 method for signature 'SingleCellExperiment' plotSmoothers( models, counts, gene, nPoints = 100, lwd = 2, size = 2/3, xlab = "Pseudotime", ylab = "Log(expression + 1)", border = TRUE, alpha = 1, sample = 1, pointCol = NULL )
models |
Either the |
... |
parameters including: |
nPoints |
The number of points used to extraplolate the fit. Defaults to 100. |
lwd |
Line width of the smoother. Passed to |
size |
Character expansion of the data points. Passed to |
xlab |
x-axis label. Passed to |
ylab |
y-axis label. Passed to |
border |
Logical: should a white border be drawn around the mean smoother. |
alpha |
Numeric between 0 and 1, determines the transparancy of data points,
see |
sample |
Numeric between 0 and 1, use to subsample the cells when there are too many so that it can plot faster. |
counts |
The matrix of gene expression counts. |
gene |
Gene name or row in count matrix of gene to plot. |
pointCol |
Plotting colors for each cell. Can be either character vector of
length 1, denoting a variable in the |
A ggplot
object
data(gamList, package = "tradeSeq") plotSmoothers(gamList[[4]])