R: Plotting (Log) Odds Ratios

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R: Plotting (Log) Odds Ratios

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plot.loddsratio {vcd}R Documentation Plotting (Log) Odds Ratios Description

Produces a (conditional) line plot of extended (log) odds ratios.

Usage ## S3 method for class 'loddsratio' plot(x, baseline = TRUE, gp_baseline = gpar(lty = 2), lines = TRUE, lwd_lines = 3, confidence = TRUE, conf_level = 0.95, lwd_confidence = 2, whiskers = 0, transpose = FALSE, col = NULL, cex = 0.8, pch = NULL, bars = NULL, gp_bars = gpar(fill = "lightgray", alpha = 0.5), bar_width = unit(0.05, "npc"), legend = TRUE, legend_pos = "topright", legend_inset = c(0, 0), legend_vgap = unit(0.5, "lines"), gp_legend_frame = gpar(lwd = 1, col = "black"), gp_legend_title = gpar(fontface = "bold"), gp_legend = gpar(), legend_lwd = 1, legend_size = 1, xlab = NULL, ylab = NULL, xlim = NULL, ylim = NULL, main = NULL, gp_main = gpar(fontsize = 12, fontface = "bold"), newpage = TRUE, pop = FALSE, return_grob = FALSE, add = FALSE, prefix = "", ...) ## S3 method for class 'loddsratio' lines(x, legend = FALSE, confidence = FALSE, cex = 0, ...) Arguments x

an object of class loddsratio.

baseline

if TRUE, a dashed line is plotted at a value of 1 (in case of odds) or 0 (in case of log-odds).

gp_baseline

object of class "gpar" used for the baseline.

lines

if TRUE, the points are connected by lines (only sensible if the variable represented by the x-axis is ordinal).

lwd_lines

Width of the connecting lines (in char units).

confidence

logical; shall confindence intervals be plotted?

conf_level

confidence level used for confidence intervals.

lwd_confidence

Line width of the confidence interval bars (in char units).

whiskers

width of the confidence interval whiskers.

transpose

if TRUE, the plot is transposed.

col

character vector specifying the colors of the fitted lines, by default chosen with rainbow_hcl.

cex

size of the plot symbols (in lines).

pch

character or numeric vector of symbols used for plotting the (possibly conditioned) observed values, recycled as needed.

bars

logical; shall bars be plotted additionally to the points? Defaults to TRUE in case of only one conditioning variable.

gp_bars

object of class "gpar" used for the bars.

bar_width

Width of the bars, if drawn.

legend

logical; if TRUE (default), a legend is drawn.

legend_pos

numeric vector of length 2, specifying x and y coordinates of the legend, or a character string (e.g., "topleft", "center" etc.). Defaults to "topleft" if the fitted curve's slope is positive, and "topright" else.

legend_inset

numeric vector or length 2 specifying the inset from the legend's x and y coordinates in npc units.

legend_vgap

vertical space between the legend's line entries.

gp_legend_frame

object of class "gpar" used for the legend frame.

gp_legend_title

object of class "gpar" used for the legend title.

gp_legend

object of class "gpar" used for the legend defaults.

legend_lwd

line width used in the legend for the different groups.

legend_size

size used for the group symbols (in char units).

xlab

label for the x-axis. Defaults to "Strata" if transpose is FALSE.

ylab

label for the y-axis. Defaults to "Strata" if transpose is TRUE.

xlim

x-axis limits. Ignored if transpose is FALSE.

ylim

y-axis limits. Ignored if transpose is TRUE.

main

user-specified main title.

gp_main

object of class "gpar" used for the main title.

newpage

logical; if TRUE, the plot is drawn on a new page.

pop

logical; if TRUE, all newly generated viewports are popped after plotting.

return_grob

logical. Should a snapshot of the display be returned as a grid grob?

add

logical; should the plot added to an existing log odds ratio plot?

prefix

character string used as prefix for the viewport name.

...

other graphics parameters (see par).

Details

The function basically produces conditioned line plots of the (log) odds ratios structure provided in x.

The lines method can be used to overlay different plots (for example, observed and expected values).

cotabplot can be used for stratified analyses (see examples).

Value

if return_grob is TRUE, a grob object corresponding to the plot. NULL (invisibly) else.

Author(s)

David Meyer [email protected]

References

M. Friendly (2000), Visualizing Categorical Data. SAS Institute, Cary, NC.