Description Usage Arguments Value
View source: R/regression_plots.R
Tools for visualizing gene signals for sveral ranked genes and display their ranking informations.
produce one 3D plot per gene in querry. Each plot is a 3D representation (low dimensionnal provided in the object warpDEDataSet
) of the dataset with cells colored by gene level expression.
1 2 3 4 5 | plot_genes(data, ranking, genes.subset = NULL, order = "head",
nb.show = 8, reg.f = "loess", span = 0.75, s.df = 4, null.model = F,
grid.size = NULL)
plot3d_genes(data, genes.subset, low.dim)
|
data |
a |
ranking |
a |
genes.subset |
character vector, let the user specifies the names of the genes of interest (default is NULL). |
order |
character, "head" (default), "tail" : specify if we want to see the |
nb.show |
numeric, number of genes displayed if genes.subset = NULL (default is 8).. |
reg.f |
a function to perform regression, either "ns" for natural splines, "loess" or "splines" (default is "loess"). |
span |
numeric, a smoothing parameter for the regression function (default is 0.75, see |
s.df |
numeric, a smoothing parameter for the nsplines regregression (default is 4, see |
null.model |
logical, if the plot of null model is wanted (default is FALSE). |
grid.size |
2 by 2 vector, for the number of rows and the number of columns that we want for the plot (the size of grid must #' be greater than the number of genes of interest), default is NULL for a squared grid. |
low.dim |
array, a 3D dimensionnal representation of the scRNA-Seq data. We expect an array of dimension (N x 3) where N is the number of cells in the experiment. |
data |
a |
genes.subset |
character vector, let the user specifies the names of the genes of interest (default is NULL). |
a visualization of the genes of interest.
a visualization of the genes of interest.
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