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Plot barcode hit

Source: R/plot_barcode_hit.R
plot_barcode_hit.Rd

Create a barcode plot for a hit. A barcode plot displays if the hit is differentially up or down regulated. If most of the vertical line are on the left side the gene associated to the barcodes is down regulated otherwise is up regulated.

Usage

plot_barcode_hit(
  screenR_Object,
  matrix_model,
  contrast,
  number_barcode = 3,
  gene,
  quantile = c(-0.5, 0.5),
  labels = c("Negative logFC", "Positive logFC")
)

Arguments

screenR_Object

The ScreenR object obtained using the create_screenr_object

matrix_model

The matrix that will be used to perform the linear model analysis. It is created using model.matrix.

contrast

An object created with makeContrasts function.

number_barcode

Number of barcode that as to be differentially expressed (DE) in order to consider the associated gene DE. Example a gene is associated with 10 shRNA we consider a gene DE if it has at least number_barcode = 5 shRNA DE.

gene

The name of the gene that has to be plot

quantile

Quantile to display on the plot

labels

The label to be displayed on the quantile side

Value

The barcode plot

Examples

object <- get0("object", envir = asNamespace("ScreenR"))
matrix_model <- model.matrix(~ slot(object, "groups"))
colnames(matrix_model) <- c("Control", "T1_T2", "Treated")
contrast <- limma::makeContrasts(Treated - Control, levels = matrix_model)

plot_barcode_hit(object, matrix_model,
    contrast = contrast,
    gene = "Gene_300"
)
#> Using classic mode.

#> NULL