cell_state_graph_plot: Plot cell state graph

In juliendelile/Antler: ANother Transcriptome Lineage ExploreR

Description

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.

juliendelile/Antler documentation built on June 19, 2021, 9 a.m.