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Plot the normalized counts of genes in each sample

Source: R/plot_boxplot.R
plot_boxplot.Rd

Draws, for the given genes, a box plot (or violin plot) of the normalized counts of their barcodes in each sample, taken from the data table. It shows the overall trend of a gene and whether it is depleted or enriched.

Usage

plot_boxplot(
  screenR_Object,
  genes,
  group_var,
  alpha = 0.5,
  nrow = NULL,
  ncol = NULL,
  fill_var = "Sample",
  type = "boxplot",
  scales = "free",
  palette = NULL
)

Arguments

screenR_Object

The ScreenR object obtained using create_screenr_object.

genes

The names of the genes to plot.

group_var

The values of the Treatment column of the data table (see get_sample_table) of the samples to plot.

alpha

Not used.

nrow

The number of rows of panels, when several genes are plotted.

ncol

The number of columns of panels, when several genes are plotted. By default (NULL) ggplot2 chooses nrow and ncol.

fill_var

The column of the data table used to fill the boxes, for example "Sample" (default), "Day" or "Treatment".

type

The type of plot: "boxplot" (default) or "violinplot".

scales

The scales of the panels: "free" (default), "fixed", "free_x" or "free_y".

palette

An optional vector of colors for the values of fill_var, which replaces the palette of the object. By default the palette of the object for fill_var is used when it is set (see get_palettes), otherwise the default colors of ggplot2.

Value

A ggplot object.

See also

plot_trend, compute_data_table

Examples

object <- get0("object", envir = asNamespace("ScreenR"))

plot_boxplot(object,
    genes = c("Gene_34"),
    group_var = c("T1", "T2", "TRT"), nrow = 1, ncol = 2,
    fill_var = "Day", type = "violinplot"
)