plot.misty.object: Plots misty.object object
In misty: Miscellaneous Functions 'T. Yanagida'

plot.misty.object

R Documentation

Plots misty.object object

Description

This function plots an misty.object object.

Usage

## S3 method for class 'misty.object'
plot(x, plot = x$args$plot, bar = x$args$bar,
     box = x$args$box, violin = x$args$violin, hist = x$args$hist,
     point = x$args$point, line = x$args$line, ci = x$args$ci,
     conf.level = x$args$conf.level, adjust = x$args$adjust,
     jitter = x$args$jitter, density = x$args$density,
     square = x$args$square, rotate = x$args$rotate,
     binwidth = x$args$binwidth, bins = x$args$bins,
     fill = x$args$fill, hist.alpha = x$args$hist.alpha,
     tile.alpha = x$args$tile.alpha, violin.alpha = x$args$violin.alpha,
     violin.trim = x$args$violin.trim, box.width = x$args$box.width,
     box.alpha = x$args$box.alpha, linetype = x$args$linetype,
     linewidth = x$args$linewidth, line.col = x$args$line.col,
     intercept = x$args$intercept, density.col = x$args$density.col,
     density.linewidth = x$args$density.linewidth,
     density.linetype = x$args$density.linetype,
     point.size = x$args$point.size, point.linewidth = x$args$point.linewidth,
     point.linetype = x$args$point.linetype,
     point.shape = x$args$point.shape, point.col = x$args$point.col,
     ci.col = x$args$ci.col, ci.linewidth = x$args$ci.linewidth,
     ci.linetype = x$args$ci.linetype, errorbar.width = x$args$errorbar.width,
     dodge.width = x$args$dodge.width, jitter.size = x$args$jitter.size,
     jitter.width = x$args$jitter.width, jitter.height = x$args$jitter.height,
     jitter.alpha = x$args$jitter.alpha, gray = x$args$gray,
     start = x$args$start, end = x$args$end, color = x$args$color,
     xlab = x$args$xlab, ylab = x$args$ylab,
     xlim = x$args$xlim, ylim = x$args$ylim,
     xbreaks = x$args$xbreaks, ybreaks = x$args$ybreaks,
     axis.title.size = x$args$axis.title.sizes,
     axis.text.size = x$args$axis.text.size,
     strip.text.size = x$args$strip.text.size, title = x$args$title,
     subtitle = x$args$subtitle, group.col = x$args$group.col,
     plot.margin = x$args$plot.margin, legend.title = x$args$legend.title,
     legend.position = x$args$legend.position,
     legend.box.margin = x$args$legend.box.margin,
     legend.key.size = x$args$legend.key.size,
     legend.text.size = x$args$legend.text.size,
     facet.ncol = x$args$facet.ncol, facet.nrow = x$args$facet.nrow,
     facet.scales = x$args$facet.scales, filename = x$args$filename,
     width = x$args$width, height = x$args$height, units = x$args$units,
     dpi = x$args$dpi, check = TRUE, ...)

Arguments

`x`	`misty.object` object.
`plot`	see 'Details'
`bar`	see 'Details'
`box`	see 'Details'
`violin`	see 'Details'
`hist`	see 'Details'
`point`	see 'Details'
`line`	see 'Details'
`ci`	see 'Details'
`conf.level`	see 'Details'
`adjust`	see 'Details'
`jitter`	see 'Details'
`density`	see 'Details'
`square`	see 'Details'
`rotate`	see 'Details'
`binwidth`	see 'Details'
`bins`	see 'Details'
`fill`	see 'Details'
`hist.alpha`	see 'Details'
`tile.alpha`	see 'Details'
`violin.alpha`	see 'Details'
`violin.trim`	see 'Details'
`box.width`	see 'Details'
`box.alpha`	see 'Details'
`linetype`	see 'Details'
`linewidth`	see 'Details'
`line.col`	see 'Details'
`intercept`	see 'Details'
`density.col`	see 'Details'
`density.linewidth`	see 'Details'
`density.linetype`	see 'Details'
`point.size`	see 'Details'
`point.linewidth`	see 'Details'
`point.linetype`	see 'Details'
`point.shape`	see 'Details'
`point.col`	see 'Details'
`ci.col`	see 'Details'
`ci.linewidth`	see 'Details'
`ci.linetype`	see 'Details'
`errorbar.width`	see 'Details'
`dodge.width`	see 'Details'
`jitter.size`	see 'Details'
`jitter.width`	see 'Details'
`jitter.height`	see 'Details'
`jitter.alpha`	see 'Details'
`gray`	see 'Details'
`start`	see 'Details'
`end`	see 'Details'
`color`	see 'Details'
`xlab`	see 'Details'
`ylab`	see 'Details'
`xlim`	see 'Details'
`ylim`	see 'Details'
`xbreaks`	see 'Details'
`ybreaks`	see 'Details'
`axis.title.size`	see 'Details'
`axis.text.size`	see 'Details'
`strip.text.size`	see 'Details'
`title`	see 'Details'
`subtitle`	see 'Details'
`group.col`	see 'Details'
`plot.margin`	see 'Details'
`legend.title`	see 'Details'
`legend.position`	see 'Details'
`legend.box.margin`	see 'Details'
`legend.key.size`	see 'Details'
`legend.text.size`	see 'Details'
`facet.ncol`	see 'Details'
`facet.nrow`	see 'Details'
`facet.scales`	see 'Details'
`filename`	a character string indicating the `filename` argument including the file extension in the `ggsave` function. Note that one of `".eps"`, `".ps"`, `".tex"`, `".pdf"` (default), `".jpeg"`, `".tiff"`, `".png"`, `".bmp"`, `".svg"` or `".wmf"` needs to be specified as file extension in the `file` argument.
`width`	a numeric value indicating the `width` argument for the `ggsave` function.
`height`	a numeric value indicating the `height` argument (default is the size of the current graphics device) for the `ggsave` function.
`units`	a character string indicating the `units` argument in the `ggsave` function. Note that one of `"in"`, `"cm"`, `"mm"`, or `"px"` needs to be specified.
`dpi`	a numeric value indicating the `dpi` argument for the `ggsave` function.
`check`	logical: if `TRUE` (default), argument specification is checked.
`...`	further arguments passed to or from other methods.

Details

This function provides plotting arguments depending on the type of the output object specified for the argument x:

Output object from aov.b, aov.w, and test.welch Function

The plot function for the misty object of type "aov.b", "aov.w", and "test.welch" has following plotting arguments:

bar: logical: if TRUE (default), bars representing means for each groups are drawn. Note that this argument is only available for the misty object of type "aov.b" and "test.welch".
point: logical: if TRUE, points representing means for each groups are drawn.
line: logical: if TRUE (default), a line connecting means of each groups and lines connecting data points are drawn when jitter = TRUE. Note that this argument is only available for misty object of type "aov.w".
ci: logical: if TRUE (default), error bars representing confidence intervals are drawn.
jitter: jittered data points are drawn. Note that subject-specific lines are also drawn for the "aov.w" function when line = TRUE.
conf.level: a numeric value between 0 and 1 (default: 0.95) indicating the confidence level of the interval.
adjust: logical: if TRUE (default), difference-adjustment for the confidence intervals in a two-sample design is applied.
point.size: a numeric value indicating the size (default: 3) aesthetic for the point representing the mean value.
line.width: a numeric value (default: 0.5) indicating the linewidth aesthetic for the line connecting means of each Groups. Note that this argument is only available for the "aov.w" function.
errorbar.width: a numeric value (default: 0.1) indicating the horizontal bar width of the error bar.
jitter.size: a numeric value (default: 1.25) indicating the size aesthetic for the jittered data points.
jitter.width: a numeric value (default: 0.05) indicating the amount of horizontal jitter.
jitter.height: a numeric value (default: 0) indicating the amount of vertical jitter.
jitter.alpha: a numeric value between 0 and 1 (default: 0.1) for specifying the alpha argument in the geom_jitter function for controlling the opacity of the jittered data points.
xlab: a character string (default: NULL) specifying the labels for the x-axis.
ylab: a character string (default: "y") specifying the labels for the y-axis.
ylim: a numeric vector of length two (default: NULL) specifying limits of the limits of the y-axis.
ybreaks: a numeric vector (default: waiver()) specifying the points at which tick-marks are drawn at the y-axis.
title: a character string (default: "") specifying the text for the title for the plot.
subtitle: a character string (default: "Two-Sided Confidence Interval" when adjust = FALSE or "Two-Sided Difference-Adjusted Confidence Interval" for the aov.b function and "Two-Sided Difference-Adjusted Cousineau-Morey Confidence Interval Confidence Interval" for the aov.w function when adjust = TRUE) specifying the text for the subtitle for the plot.
filename: character string indicating the filename argument including the file extension in the ggsave function.
width: a numeric value indicating the width argument for the ggsave function.
height: a numeric value indicating the height argument for the ggsave function.
dpi: a numeric value indicating the dpi argument for the ggsave function.
units: a character string (default: "in") indicating the units argument (default: in) for the ggsave function.

Output object from ci.* Functions

The plot function for the misty object of type "ci.cor", "ci.mean", "ci.median", "ci.prop", "ci.var", and "ci.sd" has following plotting arguments:

plot: a character string indicating the type of the plot to display, i.e., "ci" (default) for displaying confidence intervals or "boot" for displaying bootstrap samples with histograms and density curves when the argument.
hist: logical: if TRUE (default), histograms are drawn when plot = "boot".
density: logical: if TRUE (default), density curves are drawn when plot = "boot".
point: logical: if TRUE (default), vertical lines representing the point estimate are drawn when plot = "boot".
ci: logical: if TRUE (default), vertical lines representing the bootstrap confidence intervals are drawn when plot = "boot".
line: logical: if TRUE (default), a horizontal line is drawn when plot = "ci" or a vertical line is drawn when plot = "boot".
point.size: a numeric value (default: 2.5) indicating the size argument in the geom_point function for controlling the size of points when plotting confidence intervals (plot = "ci").
point.shape: a numeric value between 0 and 25 (default: 19) or a character string as plotting symbol indicating the shape argument in the geom_point function for controlling the symbols of points when plotting confidence intervals (plot = "ci").
errorbar.width: a numeric value (default: 0.3) indicating the width argument in the geom_errorbar function for controlling the width of the whiskers in the geom_errorbar function when plotting confidence intervals (plot = "ci").
dodge.width: a numeric value (default: 0.5) indicating the width argument controlling the width of the geom elements to be dodged when specifying a grouping variable using the argument group when plotting confidence intervals (plot = "ci").
binwidth: a numeric value or a function (default: NULL) for specifying the
bins: a numeric value for specifying the bins argument in the geom_histogram function for controlling the number of bins when plotting bootstrap samples (plot = "boot").
hist.alpha: a numeric value between 0 and 1 (default: 0.4) for specifying the alpha argument in the geom_histogram function for controlling the opacity of the bars when plotting bootstrap samples (plot = "boot").
fill: a character string (default: "gray85") specifying the fill argument in the geom_histogram function controlling the fill aesthetic when plotting bootstrap samples (plot = "boot"). Note that this argument applied only when no grouping variable was specified group = NULL.
density.col: a character string (default: "#0072B2") specifying the color argument in the geom_density function controlling the color of the density curves when plotting bootstrap samples (plot = "boot"). Note that this argument applied only when no grouping variable was specified group = NULL.
density.linewidth: a numeric value (default: 0.5) specifying the linewidth argument in the geom_density function controlling the line width of the density curves when plotting bootstrap samples (plot = "boot").
density.linetype: a numeric value or character string (default: 0.5) specifying the linetype argument in the geom_density function controlling the line type of the density curves when plotting bootstrap samples (plot = "boot").
point.col: a character string (default: "#CC79A7") specifying the color argument in the geom_vline function for controlling the color of the vertical line displaying the point estimate when plotting bootstrap samples (plot = "boot"). Note that this argument applied only when no grouping variable was specified group = NULL.
point.linewidth: a numeric value (default: 0.6) specifying the linewdith argument in the geom_vline function for controlling the line width of the vertical line displaying the point estimate when plotting bootstrap samples (plot = "boot").
point.linetype: a numeric value or character string (default: "solid") specifying the linetype argument in the geom_vline function controlling the line type of the vertical line displaying the point estimate when plotting bootstrap samples (plot = "boot").
ci.col: character string (default: "black") specifying the color argument in the geom_vline function for controlling the color of the vertical line displaying bootstrap confidence intervals when plotting bootstrap samples (plot = "boot"). Note that this argument applied only when no grouping variable was specified group = NULL.
ci.linewidth: a numeric value (default: 0.6) specifying the linewdith argument in the geom_vline function for controlling the line width of the vertical line displaying bootstrap confidence intervals when plotting bootstrap samples (plot = "boot").
ci.linetype: a numeric value or character string (default: "dashed") specifying the linetype argument in the geom_vline function controlling the line type of the vertical line displaying bootstrap confidence intervals when plotting bootstrap samples (plot = "boot").
intercept: a numeric value (default = 0) indicating the yintercept or xintercept argument in the geom_hline or geom_vline function controlling the position of the horizontal or vertical line when plot = "ci" and line = TRUE or when plot = "boot" and line = TRUE.
linetype: a character string (default: "solid") indicating the linetype argument in the geom_hline or geom_vline function controlling the line type of the horizontal or vertical line
line.col: a character string (default: "gray65") indicating the color argument in the geom_hline or geom_vline function for controlling the color of the horizontal or vertical line.
xlab: a character string indicating the name argument in the scale_x_continuous function for labeling the x-axis. The default setting is xlab = NULL when plot = "ci" and xlab = "Correlation Coefficient", xlab = "Arithmetic Mean", xlab = "Median", xlab = "Proportion", xlab = "Variance", or xlab = "Standard Deviation".
ylab: a character string indicating the name argument in the scale_y_continuous function for labeling the y-axis. The default setting is ylab = "Correlation Coefficient", ylab = "Arithmetic Mean", ylab = "Median", ylab = "Proportion", ylab = "Variance", or ylab = "Standard Deviation" when plot = "ci" and ylab = "Probability Density f(x)" when plot = "boot".
xlim: a numeric vector with two elements indicating the limits argument in the scale_x_continuous function for controlling the scale range of the x-axis. The default setting is xlim = NULL when plot = "ci" and xlim = c(-1, 1) for the correlation coefficient and proportion or xlim = NULL) for the arithmetic mean, median, variance and standard deviation when plot = "boot".
ylim: a numeric vector with two elements indicating the limits argument in the scale_y_continuous function for controlling the scale range of the y-axis. The default setting is ylim = c(-1, 1) fpr the correlation coefficient and proportion and ylim = NULL for the arithmetic mean, median, variance and standard deviation when plot = "ci" and xlim = NULL when plot = "boot".
xbreaks: a numeric vector (default: waiver()) indicating the breaks argument in the scale_x_continuous function for controlling the x-axis breaks.
ybreaks: a numeric vector (default: waiver()) indicating the breaks argument in the scale_y_continuous function for controlling the y-axis breaks.
axis.title.size: a numeric value (default: 11) indicating the size argument in the element_text function for specifying the function controlling the font size of the axis title, i.e. theme(axis.title = element_text(size = axis.text.size))
axis.text.size: a numeric value (default: 10) indicating the size argument in the element_text function for specifying the function controlling the font size of the axis text, i.e. theme(axis.text = element_text(size = axis.text.size)).
strip.text.size: a numeric value (default: 11) indicating the size argument in the element_text function for specifying the function controlling the font size of the strip text, i.e. theme(strip.text = element_text(size = strip.text.size)).
title: a character string (default: NULL) indicating the title argument in the labs function for the subtitle of the plot.
subtitle: a character string (default: NULL) indicating the subtite argument in the labs function for the subtitle of the plot.
group.col: a character vector (default: NULL) indicating the color argument in the scale_color_manual and scale_fill_manual functions when specifying a grouping variable using the argument group.
plot.margin: a numeric vector (default: NA) with four elements indicating the plot.margin argument in the theme function controlling the plot margins. The default setting is c(5.5, 5.5, 5.5, 5.5) but switches to c(5.5, 5.5, -2.5, 5.5) when specifying a grouping variable using the argument group.
legend.title: a character string (default: "") indicating the color argument in the labs function for specifying the legend title when specifying a grouping variable using the argument group.
legend.position: a character string (default: "bottom") indicating the legend.position in the theme argument for controlling the position of the legend function when specifying a grouping variable using the argument group.
legend.box.margin: a numeric vector (default: c(-10, 0, 0, 0)) with four elements indicating the legend.box.margin argument in the theme function for controlling the margins around the full legend area when specifying a grouping variable using the argument group.
facet.ncol: a numeric value (default: NULL) indicating the ncol argument in the facet_wrap function for controlling the number of columns when specifying a split variable using the argument split.
facet.nrow: a numeric value (default: NULL) indicating the nrow argument in the facet_wrap function for controlling the number of rows when specifying a split variable using the argument split.
facet.scales: a character string (default: "free_y") indicating the scales argument in the facet_wrap function for controlling the scales shared across facets i.e. "fixed", "free_x", "free_y" (default) or "free" when specifying a split variable using the argument split.
filename: character string indicating the filename argument including the file extension in the ggsave function.
width: a numeric value indicating the width argument for the ggsave function.
height: a numeric value indicating the height argument for the ggsave function.
dpi: a numeric value indicating the dpi argument for the ggsave function.
units: a character string (default: "in") indicating the units argument (default: in) for the ggsave function.

Output object from test.levene Function

The plot function for the misty object of type "test.levene" has following plotting arguments:

violin.alpha: a numeric value between 0 and 1 (default: 0.3) for specifying the alpha argument in the geom_violin function for controlling the opacity of the violins.
violin.trim: logical: if TRUE (default: FALSE), the tails of the violins to the range of the data is trimmed.
box.alpha: a numeric value between 0 and 1 (default: 0.2) for specifying the alpha argument in the geom_boxplot function for controlling the opacity of the boxplots.
box.width: a numeric value between 0 and 1 (default: 0.2) for specifying the alpha argument in the geom_boxplot function for controlling the opacity of the boxplots.
jitter.size: a numeric value (default: 1.25) indicating the size aesthetic for the jittered data points.
jitter.width: a numeric value (default: 0.05) indicating the amount of horizontal jitter.
jitter.height: a numeric value (default: 0) indicating the amount of vertical jitter.
jitter.alpha: a numeric value between 0 and 1 (default: 0.2) for specifying the alpha argument in the geom_jitter function for controlling the opacity of the jittered data points.
start: a numeric value between 0 and 1 (default: 0.9), graphical parameter to specify the gray value at the low end of the palette.
end: a numeric value between 0 and 1 (default: 0.4), graphical parameter to specify the gray value at the high end of the palette.
color: a character vector (default: NULL), indicating the color of the violins and the boxes. By default, default ggplot2 colors are used.
xlab: a character string (default: NULL) specifying the labels for the x-axis.
ylab: a character string (default: NULL) specifying the labels for the y-axis.
ylim: a numeric vector (default: NULL) of length two specifying limits of the limits of the y-axis.
ybreaks: a numeric vector (default: waiver()) specifying the points at which tick-marks are drawn at the y-axis.
title: a character string (default: "") specifying the text for the title for the plot.
subtitle: a character string (default: "") specifying the text for the subtitle for the plot.
filename: character string indicating the filename argument including the file extension in the ggsave function.
width: a numeric value indicating the width argument for the ggsave function.
height: a numeric value indicating the height argument for the ggsave function.
dpi: a numeric value indicating the dpi argument for the ggsave function.
units: a character string (default: "in") indicating the units argument (default: in) for the ggsave function.

Output Object from test.t and test.z Function

The plot function for the misty object of type "test.t" and "test.z" has following plotting arguments:

bar: logical: if TRUE (default), bars representing means for each groups are drawn.
point: logical: if TRUE, points representing means for each groups are drawn.
ci: logical: if TRUE (default), error bars representing confidence intervals are drawn.
jitter: logical: if TRUE, jittered data points are drawn.
line: logical: if TRUE (default), a horizontal line is drawn at mu for the one-sample t- or z-test or at 0 for the paired-sample t- or z-test.
conf.level: a numeric value between 0 and 1 (default: 0.95) indicating the confidence level of the interval.
adjust: logical: if TRUE (default), difference-adjustment for the confidence intervals in a two-sample design is applied.
point.size: a numeric value indicating the size (default: 3) aesthetic for the point representing the mean value.
errorbar.width: a numeric value (default: 0.1) indicating the horizontal bar width of the error bar.
linetype: an integer value or character string (default: 3) specifying the line type for the line representing the population mean under the null hypothesis, i.e., 0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, or 6 = twodash.
linewidth: a numeric value indicating the linewidth (default: 0.8 aesthetic for the line representing the population mean under the null hypothesis.
jitter.size: a numeric value (default: 1.25) indicating the size aesthetic for the jittered data points.
jitter.width: a numeric value (default: 0.05) indicating the amount of horizontal jitter.
jitter.height: a numeric value (default: 0) indicating the amount of vertical jitter.
jitter.alpha: a numeric value between 0 and 1 (default: 0.1) for specifying the alpha argument in the geom_jitter function for controlling the opacity of the jittered data points.
xlab: a character string (default: NULL) specifying the labels for the x-axis.
ylab: a character string (default: "y") specifying the labels for the y-axis.
ylim: a numeric vector of length two (default: NULL) specifying limits of the limits of the y-axis.
ybreaks: a numeric vector (default: waiver()) specifying the points at which tick-marks are drawn at the y-axis.
title: a character string (default: "") specifying the text for the title for the plot.
subtitle: a character string (default: "Two-Sided Confidence Interval" when adjust = FALSE or "Two-Sided Difference-Adjusted Confidence Interval" when adjust = TRUE) specifying the text for the subtitle for the plot.
filename: character string indicating the filename argument including the file extension in the ggsave function.
width: a numeric value indicating the width argument for the ggsave function.
height: a numeric value indicating the height argument for the ggsave function.
dpi: a numeric value indicating the dpi argument for the ggsave function.
units: a character string (default: "in") indicating the units argument (default: in) for the ggsave function.