plot_barcode_hit: Plot barcode hit

In EmanuelSoda/ScreenR: Package to Perform High Throughput Biological Screening

Plot barcode hit

Description

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"
)

EmanuelSoda/ScreenR documentation built on Sept. 29, 2023, 12:33 a.m.