Plot the trend of the barcodes of genes over time

Plots the log2 fold change of each barcode of the given genes at the different time points, one line for each barcode. It is useful to check the efficacy of each shRNA: good shRNAs of a hit should have a consistent trend over time.

Usage

plot_barcode_trend(
  list_data_measure,
  genes,
  n_col = 1,
  size_line = 1,
  color = NULL
)

Arguments

list_data_measure

The tables of compute_metrics for the different time points, as a list or already combined with bind_rows. The time points are shown in the order in which they appear.

genes

The names of the genes to plot.

n_col

The number of columns used to arrange the plots of the genes (default 1). When larger than 1 the plots are combined with wrap_plots.

size_line

The width of the lines. Default 1.

color

An optional vector of colors, one for each barcode.

Value

With n_col = 1, a list with one ggplot object for each gene; with n_col > 1, a single patchwork object combining them.

See also

compute_metrics, plot_barcode_hit, find_discordant_barcodes

Examples

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

metrics <- dplyr::bind_rows(
    compute_metrics(object,
        control = "Time3", treatment = "TRT",
        day = "Time3"
    ),
    compute_metrics(object,
        control = "Time4", treatment = "TRT",
        day = "Time4"
    )
)
# Multiple genes
plot_barcode_trend(metrics,
    genes = c("Gene_1", "Gene_50"),
    n_col = 2
)

# Single gene
plot_barcode_trend(metrics, genes = "Gene_300")
#> $Gene_300

#>