plot_genes: Plot several genes expression patterns

Description Usage Arguments Value

View source: R/regression_plots.R

Description

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.

Usage

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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)

Arguments

data

a warpDEDataSet with results to be plotted.

ranking

a rankingDE object, rankings rows of the genes of interest in the ranking dataframe.

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 first or last genes of the ranking.

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 gam::lo for details).

s.df

numeric, a smoothing parameter for the nsplines regregression (default is 4, see splines::s for details about regularization).

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 warpDEDataSet with results to be plotted.

genes.subset

character vector, let the user specifies the names of the genes of interest (default is NULL).

Value

a visualization of the genes of interest.

a visualization of the genes of interest.


strayMat/warpDE documentation built on Dec. 8, 2017, 2:42 a.m.