Plot cell state graph

Arguments

cell_colors

character vector indicating the metadata to use to color the vertices. Names can be either one of the column names of the phenotypic metadata structure (see colnames(pData(antler$expressionSet))), names of a cluster entries, or gene names. The element of the character vector can be named themselves, in that case the element name will serve as a title for phenotypic metadata or cluster entries. If gene names are specified, their vector names must indicate the type of read counts that will be used to render the expression levels: "Raw", "Normalized" or "Smoothed". If no gene name's name is specified raw level will be rendered.

labels

character vector. Labels to draw on top of the cells. Default to NA.

vertex.size

numeric vector indicating the size of the vertices representing the cells.

vertex.shape

character vector indicating the shape of the vertices. Can be either "circle" (default), "square" or "triangle".

vertex.frame.color

character vector indicating the color of the frame of each vertex. Default to NA.

edge.width

numeric value indicating the width of graph edges. Default to a fifth of the vertex size.

edge.color

character string indicating the color of the edges. Default to "grey".

width

numeric value indicating the width (in inches) of each individual subplots. Default to 3.

height

numeric value indicating the height (in inches) of each individual subplots. Default to 3.

title

logical value indicating whether to show each subplots' title. Default to TRUE.

save_pdf

logical value indicating whether to save plot as a pdf file. Default to TRUE.

shuffle

logical value indicating whether to randomize the z-order of each vertex. Default to FALSE.

vertex.plot.order

integer vector. The z-order used to render the vertices. Default to NA.

gene_palette

character string. The color palette to use if genes are specified as cell colors.

filename

character string. The filename of the output file, if any.

...

Extra arguments passed to plot.igraph.