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This function plots a boxplot for each sample for the genes passed as input. It can be used to see the overall trend of a gene and so to visualize if the gene is up or down regulated.

Usage

plot_boxplot(
  screenR_Object,
  genes,
  group_var,
  alpha = 0.5,
  nrow = 1,
  ncol = 1,
  fill_var = "Sample",
  type = "boxplot",
  scales = "free"
)

Arguments

screenR_Object

The ScreenR object obtained using the create_screenr_object

genes

The vector of genes that will be displayed

group_var

The variable that as to be used to filter the data, for example the different treatment

alpha

A value for the opacity of the plot. Allowed values are in the range 0 to 1

nrow

The number of rows in case multiple genes are plotted

ncol

The number of columns in case multiple genes are plotted

fill_var

The variable used to fill the boxplot

type

The type of plot to use "boxplot" or "violinplot"

scales

The scales used for the facet. Possible values can be "free", "fixed" and "free_y"

Value

A boxplot

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"
)