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"
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"
)
