panels: More panel plots

In SciViews/SciViews: 'SciViews' - Data Processing and Visualization with the 'SciViews::R' Dialect

More panel plots

Description

Several panel plots that can be used with coplot() and pairs().

Usage

panel_reg(
  x,
  y,
  col = par("col"),
  bg = par("bg"),
  pch = par("pch"),
  cex = par("cex"),
  lwd = par("lwd"),
  line.reg = lm,
  line.col = "red",
  line.lwd = lwd,
  untf = TRUE,
  ...
)

panel.reg(
  x,
  y,
  col = par("col"),
  bg = par("bg"),
  pch = par("pch"),
  cex = par("cex"),
  lwd = par("lwd"),
  line.reg = lm,
  line.col = "red",
  line.lwd = lwd,
  untf = TRUE,
  ...
)

panel_ellipse(
  x,
  y,
  col = par("col"),
  bg = par("bg"),
  pch = par("pch"),
  cex = par("cex"),
  el.level = 0.7,
  el.col = "cornsilk",
  el.border = "red",
  major = TRUE,
  ...
)

panel.ellipse(
  x,
  y,
  col = par("col"),
  bg = par("bg"),
  pch = par("pch"),
  cex = par("cex"),
  el.level = 0.7,
  el.col = "cornsilk",
  el.border = "red",
  major = TRUE,
  ...
)

panel_cor(
  x,
  y,
  use = "everything",
  method = c("pearson", "kendall", "spearman"),
  alternative = c("two.sided", "less", "greater"),
  digits = 2,
  prefix = "",
  cex = par("cex"),
  cor.cex = cex,
  stars.col = "red",
  ...
)

panel.cor(
  x,
  y,
  use = "everything",
  method = c("pearson", "kendall", "spearman"),
  alternative = c("two.sided", "less", "greater"),
  digits = 2,
  prefix = "",
  cex = par("cex"),
  cor.cex = cex,
  stars.col = "red",
  ...
)

panel_smooth(
  x,
  y,
  col = par("col"),
  bg = NA,
  pch = par("pch"),
  cex = 1,
  col.smooth = 2,
  span = 2/3,
  iter = 3,
  ...
)

Arguments

x	A numeric vector.
y	A numeric vector of same length as x.
col	The color of the points.
bg	The background color for symbol used for the points.
pch	The symbol used for the points.
cex	The expansion factor used for the points.
lwd	The line width.
line.reg	A function that calculates coefficients of a straight line, for instance, lm(), or rlm() for robust linear regression.
line.col	The color of the line.
line.lwd	The width of the line.
untf	Logical asking whether to untransform the straight line in case one or both axis are in log scale.
...	Further arguments to plot functions.
el.level	The confidence level for the bivariate normal ellipse around data; the default value of 0.7 draws an ellipse of roughly +/-1 sd.
el.col	The color used to fill the ellipse.
el.border	The color used to draw the border of the ellipse and the standardized major axis.
major	If TRUE, the standardized major axis is also drawn.
use	One of "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs" (can be abbreviated). Defines how the cor() function behaves with missing observations.
method	One of the three correlation coefficients "pearson" (default), "kendall", or "spearman". Can be abbreviated.
alternative	The alternative hypothesis in correlation test, see cor.test().
digits	The number of decimal digits to print when the correlation coefficient is printed in the graph.
prefix	A prefix (character string) to use before the correlation coefficient printed in the graph.
cor.cex	Expansion coefficient for text in printing correlation coefficients.
stars.col	The color used for significance stars (with: *** p < 0.001, ** p < 0.1, * p < 0.05, . p < 0.1.
col.smooth	Color to be used by lines for drawing the smooths.
span	Smoothing parameter f for lowess(), see there.
iter	Number of robustness iterations for lowess().

Details

Theses functions should be used outside of the diagonal in pairs(), or with coplot(), as they are bivariate plots.

Value

These functions return nothing and are used for their side effect of plotting in panels of composite plots.

Author(s)

Philippe Grosjean [e-mail], but code inspired from panel.smooth() in graphics and panel.car() in package car.

See Also

coplot(), pairs(), panel.smooth(), lm(), ellipse(), cor() and cor.test()

Examples

# Smooth lines in lower graphs and straight lines in upper graphs
pairs(trees, lower.panel = panel_smooth, upper.panel = panel_reg)
# Robust regression lines
library(MASS)  # For rlm()
pairs(trees, panel = panel_reg, diag.panel = panel_boxplot,
  reg.line = rlm, line.col = "blue", line.lwd = 2)
# A Double log graph
pairs(trees, lower.panel = panel_smooth, upper.panel = panel_reg, log = "xy")

# Graph suitables to explore correlations (take care there are potentially
# many simultaneous tests done here... So, you loose much power in the whole
# analysis... use it just as an indication!)
# Pearson's r
pairs(trees, lower.panel = panel_ellipse, upper.panel = panel_cor)
# Spearman's rho (ellipse and straight lines not suitable here!)
pairs(trees, lower.panel = panel_smooth, upper.panel = panel_cor,
  method = "spearman", span = 1)
# Several groups (visualize how bad it is to consider the whole set at once!)
pairs(iris[, -5], lower.panel = panel_smooth, upper.panel = panel_cor,
  method = "kendall", span = 1,
  col = c("red3", "blue3", "green3")[iris$Species])
# Now analyze correlation for one species only
pairs(iris[iris$Species == "virginica", -5], lower.panel = panel_ellipse,
  upper.panel = panel_cor)

# A coplot with custom panes
coplot(Petal.Length ~ Sepal.Length | Species, data = iris,
  panel = panel_ellipse)

SciViews/SciViews documentation built on Sept. 16, 2023, 10:26 p.m.