R/ClearScatterplot.R
createPlot-ClearScatterplot-method.Rd
Creates a plot based on the ClearScatterplot object data.
# S4 method for class 'ClearScatterplot'
createPlot(
object,
color1 = "cornflowerblue",
color2 = "grey",
color3 = "indianred",
highLog2fc = 0.585,
lowLog2fc = -0.585,
negLog10pValue = 1.301,
expressionDirection = "regulation",
negativeLogPValue = "negLog10p",
timeVariable = "reg_time_org",
xAxis = "organ",
yAxis = "timePoint"
)
A ClearScatterplot object.
Color for one category of data points.
Color for another category of data points.
Color for a third category of data points.
Threshold for high log2 fold change values.
Threshold for low log2 fold change values.
Threshold for -log10 p-value.
Direction of gene expression.
The name of the column containing the negative log p-values.
The variable representing time.
The x-axis values.
The y-axis values.
The ClearScatterplot object with the plot updated.
plotdata <- get_clear_scatterplot_df()
scatterplotObject <- ClearScatterplot(
data = plotdata,
logFoldChange = "log2fc",
timePointColumn = "timePoint",
timePointLevels = c("T10R1", "T5R1")
)
scattered_plot <- createPlot(
scatterplotObject,
color1 = "cornflowerblue",
color2 = "grey",
color3 = "indianred",
highLog2fc = 0.585,
lowLog2fc = -0.585,
negLog10pValue = 1.301,
expressionDirection = "regulation",
negativeLogPValue = "negLog10p",
timeVariable = "reg_time_org",
xAxis = "organ",
yAxis = "timePoint"
)
#> Scale for colour is already present.
#> Adding another scale for colour, which will replace the existing scale.