plot_genes_violin {monocle} | R Documentation

## Plots expression for one or more genes as a violin plot

### Description

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.

### Usage

    plot_genes_violin(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,
      relative_expr = TRUE, log_scale = TRUE)

### Arguments

`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
`log_scale` | a boolean that determines whether or not to scale data logarithmically

### Value

a ggplot2 plot object

### Examples

    ## Not run:
    library(HSMMSingleCell)
    HSMM <- load_HSMM()
    my_genes <- HSMM[row.names(subset(fData(HSMM), gene_short_name %in% c("ACTA1", "ID1", "CCNB2"))),]
    plot_genes_violin(my_genes, grouping="Hours", ncol=2, min_expr=0.1)

    ## End(Not run)

[Package monocle version 2.6.4 Index]