A class for creating and managing scatterplot objects with enhanced visualization features.

Creates an instance of the ClearScatterplot class.

ClearScatterplot(
  data,
  logFoldChange = "log2fc",
  negativeLogPValue = "negLog10p",
  highLog2fc = 0.585,
  lowLog2fc = -0.585,
  negLog10pValue = 1.301,
  timePointColumn = "timePoint",
  timePointLevels = NULL
)

Arguments

data

A data frame containing the plot data.

logFoldChange

The name of the column containing expression values.

negativeLogPValue

The column containing the negative log p-values.

highLog2fc

Threshold for high log2 fold change values.

lowLog2fc

Threshold for low log2 fold change values.

negLog10pValue

Threshold for -log10 p-value.

timePointColumn

The name of the column containing time point info.

timePointLevels

The levels for the time point column, if any.

Value

An object of class ClearScatterplot.

Slots

data

A data frame containing the data to be plotted.

plot

An object storing the ggplot representation of the data.

Examples

plotdata <- get_clear_scatterplot_df()
scatterplotObject <- ClearScatterplot(
  data = plotdata,
  logFoldChange = "log2fc",
  timePointColumn = "timePoint",
  timePointLevels = c("T10R1", "T5R1")
)