my_plot_genes_jitter: Plots expression for one or more genes as a jittered, grouped...
In efheuston/MyPlotTrajectoryPackage:

Description Usage Arguments Value Examples

Accepts a subset of a CellDataSet and an attribute to group cells by, and produces one or more ggplot2 objects that plots the level of expression for each group of cells.

my_plot_genes_jitter(cds_subset, grouping = "State", min_expr = NULL,
  cell_size = 0.75, nrow = NULL, ncol = 1, panel_order = NULL,
  color_by = NULL, plot_trend = FALSE, label_by_short_name = TRUE,
  point_colors = c("#cb4bbe", "lightskyblue", "grey37", "#53ba48", "moccasin",
  "#dcca44", "#502d70", "#afd671", "#cb4471", "#69da99", "#d44732", "#6fd3cf",
  "#5d2539", "#cfd0a0", "blue", "#d2883b", "#6793c0", "#898938", "#c98ac2",
  "yellow", "#c4c0cc", "#7d3d23", "#00a5ff", "#d68d7a", "#a2c1a3"),
  relative_expr = TRUE)

`cds_subset`	CellDataSet for the experiment
`grouping`	the cell attribute (e.g. the column of pData(cds)) to group cells by on the horizontal axis
`min_expr`	the minimum (untransformed) expression level to use in plotted the genes.
`cell_size`	the size (in points) of each cell used in the plot
`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)
`color_by`	the cell attribute (e.g. the column of pData(cds)) to be used to color each cell
`plot_trend`	whether to plot a trendline tracking the average expression across the horizontal axis.
`label_by_short_name`	label figure panels by gene_short_name (TRUE) or feature id (FALSE)
`relative_expr`	Whether to transform expression into relative values

a ggplot2 plot object

## Not run: 
library(HSMMSingleCell)
HSMM <- load_HSMM()
my_genes <- HSMM[row.names(subset(fData(HSMM), gene_short_name %in% c("MYOG", "ID1", "CCNB2"))),]
plot_genes_jitter(my_genes, grouping="Media", ncol=2)

## End(Not run)