Utility functions for adding growth standard bands to rbokeh/lattice/ggplot2 plots

Utility functions for adding growth standard bands to rbokeh/lattice/ggplot2 plots

panel.who(x, x_var = "agedays", y_var = "htcm", sex = "Female",
  p = c(1, 5, 25, 50), color = NULL, alpha = 0.15, center = FALSE,
  labels = TRUE, x_trans = identity, y_trans = identity)

panel.igb(gagebrth, var = "lencm", sex = "Female", p = c(1, 5, 25,
  50), color = NULL, alpha = 0.15, center = FALSE, labels = TRUE,
  x_trans = identity, y_trans = identity)

panel.igfet(gagedays, var = "hccm", p = c(1, 5, 25, 50),
  color = "green", alpha = 0.15, center = FALSE, labels = TRUE,
  x_trans = identity, y_trans = identity)

geom_growthstandard(mapping = NULL, data = NULL, x_seq,
  x_var = "agedays", y_var, sex = "Female", p = c(1, 5, 25, 50),
  shade = NULL, alpha = 0.15, center = FALSE, x_trans = identity,
  y_trans = identity, standard = "who", inherit.aes = TRUE)

geom_who(...)

geom_igb(..., var = "lencm")

geom_igfet(..., var = "hccm", color = "green")

ly_who(fig, x, x_var = "agedays", y_var = "htcm", sex = "Female",
  p = c(1, 5, 25, 50), color = NULL, alpha = 0.15, center = FALSE,
  labels = TRUE, x_trans = identity, y_trans = identity,
  x_units = c("days", "months", "years"))

ly_igb(fig, gagebrth, var = "lencm", sex = "Female", p = c(1, 5, 25,
  50), color = NULL, alpha = 0.15, center = FALSE, labels = TRUE,
  x_trans = identity, y_trans = identity)

ly_igfet(fig, gagedays, var = "hccm", p = c(1, 5, 25, 50),
  color = "green", alpha = 0.15, center = FALSE, labels = TRUE,
  x_trans = identity, y_trans = identity)

Arguments

x, x_seq	value or vector of values that correspond to a measure defined by x_var. x_seq is used with geom_*
x_var	x variable name (typically "agedays")
y_var	y variable name (typically "htcm" or "wtkg")
sex	"Male" or "Female"
p	centiles at which to draw the growth standard band polygons (only need to specify on one side of the median)
color, shade	optional color to use for bands (will use sex to determine if not specified). shade is used with geom_*
alpha	transparency of the bands
center	should the bands be centered around the median?
labels	should the centiles be labeled? (not implemented)
x_trans	transformation function to be applied to x-axis
y_trans	transformation function to be applied to y-axis
gagebrth	gestational age at birth in days (for igb plots)
var	variable name for y axis for igb or igfet plots ("lencm", "wtkg", or "hcircm" for igb; "accm", "bpdcm", "flcm", "hccm", or "ofdcm" for igfet)
gagedays	gestational age in days (for igfet plots)
data, mapping, inherit.aes	supplied direclty to ggplot2::layer
standard	standard name to use. Either "who", "igb", or "igfet"
...	items supplied direclty to geom_growthstandard
fig	rbokeh figure to add growth standard to
x_units	units of age x-axis (days, months, or years)

Examples

# NOT RUN {
#### rbokeh

library(rbokeh)
figure() %>%
  ly_who(x = seq(0, 2558, by = 30), y_var = "wtkg",
    x_trans = days2years, sex = "Male") %>%
  ly_points(days2years(agedays), wtkg,
    data = subset(cpp, subjid == 8), col = "black",
    hover = c(agedays, wtkg, lencm, htcm, bmi, geniq, sysbp, diabp))

cpp$wtkg50 <- who_centile2value(cpp$agedays, y_var = "wtkg")
figure() %>%
  ly_who(x = seq(0, 2558, by = 30), y_var = "wtkg", color = "blue",
    x_trans = days2years, center = TRUE) %>%
  ly_points(days2years(agedays), wtkg - wtkg50, color = "black",
    data = subset(cpp, subjid == 8))

# look at Male birth lengths superposed on INTERGROWTH birth standard
# first we need just 1 record per subject with subject-level data
cppsubj <- subset(cpp, !duplicated(cpp$subjid))
figure(xlab = "Gestational Age at Birth (days)", ylab = "Birth Length (cm)") %>%
  ly_igb(gagebrth = 250:310, var = "lencm", sex = "Male") %>%
  ly_points(jitter(gagebrth), birthlen, data = subset(cppsubj, sex == "Male"),
    color = "black")

# plot growth standard bands at z=1, 2, 3 for fetal head circumference
figure(xlab = "Gestational Age (days)",
  ylab = "Head Circumference (cm)") %>%
    ly_igfet(gagedays = 98:280, var = "hccm", p = pnorm(-3:0) * 100)
# }

#### lattice

library(lattice)
xyplot(wtkg ~ agedays, data = subset(cpp, subjid == 8),
  panel = function(x, y, ...) {
    panel.who(x = seq(0, 2558, by = 30),
      sex = "Male", y_var = "wtkg", p = 100 * pnorm(-3:0))
    panel.xyplot(x, y, ...)
  },
  col = "black"
)

# look at Male birth lengths superposed on INTERGROWTH birth standard
# first we need just 1 record per subject with subject-level data
cppsubj <- subset(cpp, !duplicated(cpp$subjid))
xyplot(birthlen ~ jitter(gagebrth), data = subset(cppsubj, sex == "Male"),
  panel = function(x, y, ...) {
    panel.igb(gagebrth = 250:310, var = "lencm", sex = "Male")
    panel.points(x, y, ...)
  },
  col = "black", alpha = 0.75,
  xlab = "Gestational Age at Birth (days)", ylab = "Birth Length (cm)"
)

#### ggplot2

library(ggplot2)
p <- ggplot(data = subset(cpp, subjid == 8), aes(x = agedays, y = htcm)) +
  geom_who(x_seq = seq(0, 2600, by = 10), y_var = "htcm") +
  geom_point()