TACS.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data_handling_seurat.R
\name{TACS}
\alias{TACS}
\title{Make a FACS-like plot from a single-cell rna-seq dataset.}
\usage{
TACS(dge, gene1, gene2, cutoffs = NULL, return_val = "plot",
  density = F, facet_by = NULL, include_panel_with_all = FALSE,
  facet_levels = FetchData(dge, facet_by)[[1]] \%>\% factor \%>\% levels
  \%>\% c(rep("all", include_panel_with_all), .),
  col = stats::setNames((scales::hue_pal())(length(facet_levels) -
  include_panel_with_all), facet_levels[(include_panel_with_all +
  1):length(facet_levels)]), num_genes_add = 100,
  genesets_predetermined = F, dge_reference = dge, ...)
}
\arguments{
\item{dge}{Seurat object}

\item{gene1}{Horizontal axis on plot mimics this gene. Character, usually length 1 but possibly longer.}

\item{gene2}{Vertical axis on plot mimics this gene. Character, usually length 1 but possibly longer.}

\item{cutoffs}{If given, divide plot into four quadrants and annotate with percentages. Numeric vector of length 2.}

\item{return_val}{If "all", returns a list with several internal calculations revealed.
If "plot", returns just a ggplot object. If "seurat", returns a Seurat object with gene scores added.}

\item{density}{If TRUE, plot contours instead of points.}

\item{num_genes_add}{Each axis shows a simple sum of similar genes. This is how many (before removing overlap). Integer.}

\item{genesets_predetermined}{If FALSE, plot the sum of many genes similar to gene1 instead of gene1 alone (same 
for gene2). See ?get_similar_genes. If TRUE, plot the sum of only the genes given.}

\item{dge_reference}{Seurat object. This function relies on gene-gene correlation. If your dataset is perturbed in a way 
that would substantially alter gene-gene correlations, for example if different time points are present or certain 
cell types are mostly depleted, you can feed in a reference dge, and TACS will choose axes based on the reference data.}

\item{...}{Extra params for stat_density2d.

This function is based on a simple scheme: choose genes similar to the ones specified 
and average them to reduce the noise.}
}
\description{
Make a FACS-like plot from a single-cell rna-seq dataset.
}