Plot PDF of Empirical Data

plotPDF() creates a plot of the smoothed kernel density estimate of the probability density function (PDF) for a numeric vector of continuous data.

plotPDFbyGroup() creates a plot with a series of smoothed density estimates of the probability density function (PDF) stratified/split by a grouping variable of (usually) meta data, e.g. Response grouping.

plotPDFlist() creates a series of plots of the smoothed kernel density estimates of the probability density function (PDF) from a numeric list object.

Usage

plotPDF(
  x,
  col = soma_colors$purple,
  x.lab = "values",
  y.lab = "Probability Density",
  main = "Kernel Density Estimate",
  lty = "solid",
  fill = FALSE,
  add.gauss = FALSE
)

plotPDFbyGroup(
  data,
  apt,
  group.var,
  cols,
  xlim = NULL,
  x.lab = bquote(italic(log)[10] ~ (RFU)),
  main = apt,
  lty = "solid",
  fill = FALSE,
  ablines = NULL,
  include.counts = FALSE
)

plotPDFlist(.data, label = "Group", main = "PDF by Group", ...)

Arguments

x

A numeric vector.

col

Character. String for the color of the line.

x.lab

Character. Optional string for the x-axis. Otherwise one is automatically generated (default).

y.lab

Character. Optional string for the y-axis. Otherwise one is automatically generated (default).

main

Character. Main title for the plot. See ggtitle() for ggplot2 style graphics.

lty

Character. Passed to geom_vline(). See ggtitle().

fill

Logical. Should shaded colors beneath the curve be added?

add.gauss

Logical. Should a Gaussian fit of the data be plotted with the PDF?

data, .data

A soma_adat or data.frame object containing RFU data.

apt

Character. The name of a column in data to use in generating CDFs. Typically an aptamer measurement.

group.var

An unquoted column name from data containing group labels.

cols

Character. A vector of colors for the groups/boxes. For plotDoubleHist(), must be length = 2.

xlim

Numeric. Limits for the x-axis. See coord_cartesian().

ablines

Numeric. A vector of x-axis position(s) for vertical lines to be added to the CDF or PDF.

include.counts

Logical. Should class counts be added to the plot legend?

label

Character. A label for the grouping variable, i.e. what the entries of the list represent.

...

Additional arguments passed to either plotCDFbyGroup() or plotPDFbyGroup(), primarily one of:

x.lab
lty
cols
xlim
fill
ablines

Examples

# `plotPDF()`
x <- rnorm(100, mean = 5)
plotPDF(x)

plotPDF(x, col = "dodgerblue")

plotPDF(x, add.gauss = TRUE)

plotPDF(x, add.gauss = TRUE, fill = TRUE)


# `plotPDFbyGroup()`
data  <- SomaDataIO::example_data |> dplyr::filter(SampleType == "Sample")
anno  <- SomaDataIO::getTargetNames(SomaDataIO::getAnalyteInfo(data))
fsh   <- "seq.3032.11"
title <- anno[[fsh]]
plotPDFbyGroup(log10(data), apt = fsh, group.var = Sex, main = title)

plotPDFbyGroup(log10(data), apt = fsh, group.var = Sex,
               fill = TRUE, main = title)

lines <- split(log10(data[[fsh]]), data$Sex) |>
  vapply(median, double(1))
plotPDFbyGroup(log10(data), apt = fsh, group.var = Sex,
               fill = TRUE, ablines = lines, main = title)


# `plotPDFlist()`
x <- withr::with_seed(101,
  mapply(mean = 3:5, n = c(10, 100, 1000), FUN = rnorm) |>
    setNames(paste0("Group", 1:3))
)
lengths(x)
#> Group1 Group2 Group3 
#>     10    100   1000 

sapply(x, mean)
#>   Group1   Group2   Group3 
#> 3.245040 3.964522 4.969620 

# warning: RFU values should all be positive!
plotPDFlist(x)

plotPDFlist(x, label = "SplitBy")

plotPDFlist(x, fill = TRUE)

plotPDFlist(x, x.lab = "My x-axis", main = "Variable `x` PDF")

medians <- vapply(x, median, 0.0)
plotPDFlist(x, ablines = medians, main = "Variable `x` PDF")

Usage

Arguments

See also

Examples