agePlotter: Age plotter

In LieberInstitute/jaffelab: Commonly used functions by the Jaffe lab

Age plotter

Description

Plots a Y output by age.

Usage

agePlotter(
  y,
  age,
  mod = matrix(rep(1, length(y)), ncol = 1),
  mainText,
  smoothIt = TRUE,
  jitter = TRUE,
  ageLabel = "bottom",
  orderByAge = TRUE,
  ylim = NULL,
  ageBreaks = c(-1, 0, 1, 10, 100),
  ylab = "Adjusted Expression",
  pointColor = 2,
  lineColor = 1,
  alreadyFitted = NULL,
  ...
)

Arguments

y	A vector with the Y outcome.
age	A vector with the age information.
mod	A model matrix.
mainText	A character vector with the main title.
smoothIt	A logical indicating whether to smooth Y.
jitter	A logical indicating whether to add jitter on the X axis.
ageLabel	The location of the age legend.
orderByAge	A logical indicating whether to sort the observations by age.
ylim	A length two vector with the Y axis limits.
ageBreaks	The age cutoffs for the different groups.
ylab	The Y axis label.
pointColor	An integer indicating the palette color to use for the points.
lineColor	An integer indicating the paletter color to use for the lines.
alreadyFitted	The output of fitted on a linear model if you already calculated it. If so, y will be ignored.
...	Additional parameters to pass to plot.

Details

pointColor can be a vector of length equal to age and have multiple values in which case lineColor has to have a length equal to the number of unique pointColor values. Specifying this will draw a line for each unique pointColor.

Value

A nice plot =)

Author(s)

Andrew E Jaffe, Leonardo Collado-Torres (examples)

Examples

def.par <- par(no.readonly = TRUE) # save default, for resetting...

## Generate some Ys
set.seed(20190827)
y <- as.vector(vapply(0:5, function(x) rnorm(20, mean = x), numeric(20)))

## Generate some ages
age <- as.vector(
    mapply(runif,
        c(-1, 0, 1, 10, 20, 50), c(0, 1, 10, 20, 50, 90),
        n = 20
    )
)

## Make the age plot with a regression line across age vs Y
agePlotter(y, age,
    mainText = "agePlotter example",
    ylab = "Random Ys",
    mod = model.matrix(~age),
    ageBreaks = c(-1, 0, 1, 10, 20, 50, 100)
)

## Define line and point colors
p_cols <- rep(rep(c("skyblue3", "dark orange"), each = 10), 6)
l_cols <- c("lightgoldenrod", "light blue")

## Make the plot with the above colors
agePlotter(y, age,
    mainText = "agePlotter example",
    ylab = "Random Ys",
    mod = model.matrix(~age),
    ageBreaks = c(-1, 0, 1, 10, 20, 50, 100),
    pointColor = p_cols,
    lineColor = l_cols
)
legend("bottom", c("DLPFC", "HIPPO"),
    col = l_cols, lwd = 3, bty = "n",
    ncol = 2
)


par(def.par) #- reset to default

LieberInstitute/jaffelab documentation built on April 1, 2024, 7:26 a.m.