my_plot_genes_positive_cells: Plots the number of cells expressing one or more genes as a...
In efheuston/MyPlotTrajectoryPackage:

Description Usage Arguments Details Value Examples

@description Accetps a CellDataSet and a parameter,"grouping", used for dividing cells into groups. Returns one or more bar graphs (one graph for each gene in the CellDataSet). Each graph shows the percentage of cells that express a gene in the in the CellDataSet for each sub-group of cells created by "grouping".

my_plot_genes_positive_cells(cds_subset, grouping = "State", min_expr = 0.1,
  nrow = NULL, ncol = 1, panel_order = NULL, plot_as_fraction = TRUE,
  label_by_short_name = TRUE, relative_expr = 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"),
  plot_limits = c(0, 100))

`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.
`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)
`plot_as_fraction`	whether to show the percent instead of the number of cells expressing each gene
`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
`plot_limits`	A pair of number specifying the limits of the y axis. If NULL, scale to the range of the data.

Let's say the CellDataSet passed in included genes A, B, and C and the "grouping parameter divided all of the cells into three groups called X, Y, and Z. Then three graphs would be produced called A, B, and C. In the A graph there would be three bars one for X, one for Y, and one for Z. So X bar in the A graph would show the percentage of cells in the X group that express gene A.

a ggplot2 plot object

## Not run: 
library(HSMMSingleCell)
HSMM <- load_HSMM()
MYOG_ID1 <- HSMM[row.names(subset(fData(HSMM), gene_short_name %in% c("MYOG", "ID1"))),]
plot_genes_positive_cells(MYOG_ID1, grouping="Media", ncol=2)

## End(Not run)