gene_jitterplot: Plot expression of cells as jitter plot
In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description Usage Arguments Value Examples

gene_jitterplot() plots the expression of a given gene as a jitter plot for a CellDataSet object.

gene_jitterplot(genes, cds, group = "genotype", color = NULL,
  cell_size = 0.75, exprs_threshold = 0, nrow = NULL, ncol = 1,
  panel_order = NULL, gene_groups = NULL, plot_trend = FALSE,
  color_trend = "orange", label_by_short_name = TRUE,
  log_expr = TRUE, relative_expr = FALSE, scales = "free_y")

`genes`	a vector of gene name(s) to plot e.g. c("Actb", "Aldoa")
`cds`	a CellDataSet object e.g. used in the monocle package
`group`	column name in pData(cds) to group cells by on the horizontal axis.
`color`	column name in pData(cds) to color cells with.
`cell_size`	the size (in points) of each cell used in the plot
`exprs_threshold`	the (untransformed) expression threshold to use in plotting genes; expression values less than or equal to this threshold will be converted to 0
`nrow`	the number of rows used when laying out the panels for each gene's expression
`ncol`	the number of columns used when laying out the panels for each gene's expression
`panel_order`	the order in which genes should be layed out (left-to-right, top-to-bottom)
`gene_groups`	dataframe specifying groups for genes to be plotted; first column should be gene id or gene short name (if label_by_short_name = T), and second column should be group id for gene; can be used for facet_wrap or color by using the variable "gene_group"
`plot_trend`	logical;whether to plot a trend line across groups in plot(s).
`color_trend`	color to use for trend line.
`label_by_short_name`	logical;label figure panels by gene_short_name (TRUE) or feature id (FALSE)
`log_expr`	logical; whether to log-transform expression into log10(expression + 1)
`relative_expr`	logical;Whether to transform expression into counts per 10,000
`scales`	input for facet_wrap scale; options include "free_y" or "fixed"