diffplot {canprot} | R Documentation |
Plot Differences of Chemical Metrics
Description
Make a plot showing differences of selected chemical metrics.
Usage
diffplot(comptab, vars = c("ZC", "nH2O"), col = "black", plot.rect = FALSE,
pt.text = c(letters, LETTERS), cex.text = 0.85, oldstyle = FALSE,
pch = 1, cex = 2.1, contour = TRUE, col.contour = par("fg"),
probs = 0.5, add = FALSE, labtext = NULL, ...)
cplab
Arguments
comptab |
list or data frame, chemical differences generated by |
vars |
character, which variables to plot |
col |
character or numeric, color(s) for the points |
plot.rect |
logical, plot a reference rectangle? |
pt.text |
character, text labels for the points |
cex.text |
numeric, size of text labels |
oldstyle |
logical, use old style plot? |
pch |
numeric, point symbol |
cex |
numeric, point size |
contour |
logical, add contour lines? |
col.contour |
character or numeric, color of contour lines |
probs |
numeric, probability level(s) for contours |
add |
logical, add to an existing plot? |
labtext |
character, text to add to axis labels |
... |
other argumenents passed to |
Details
A plot is created with points showing the differences between up- and down-regulated proteins for two chemical metrics, as calculated by get_comptab
.
The default setting of vars
refers to average oxidation state of carbon (ZC) as the x-variable and stoichiometric hydration state (nH2O) as the y-variable.
The colors of the points are controlled by col
, which is recycled to be equal to the number of comparisons in comptab
.
If plot.rect
is TRUE, a shaded rect
angle is drawn with coordinates -0.01, -0.01, 0.01, 0.01.
This is useful for visualizing the different scales of multi-panel plots.
If pt.text
is not NA or FALSE, text
labels are added with size controlled by cex.text
.
The default value produces labels that are taken sequentially from the 26 lowercase Roman letters in alphabetical order (letters
), followed by the set of uppercase letters (LETTERS
).
For labtext
= NULL, descriptive text (“median difference” or “mean difference”) is added to the axis labels in parentheses.
This text can be changed by giving a value in labtext
(for both axes), two values (for each axis), or NA to suppress the text.
cplab
is a list of formatted labels used by diffplot
.
It is an exported object, available to the user and other packages.
Plot style
The overall style of the plot is controlled by oldstyle
.
oldstyle = FALSE
-
This is the current default style. Use
pch
andcex
to control the point symbol and size. Contours are added for confidence regions of highest probability density, computed using a 2-D kernel density estimate (kde2d
).probs
gives the probability level(s) andcol.contour
sets the color(s) of the contour lines.contour
can be a logical vector, indicating which points to include; set it to FALSE to omit the contour lines.The code to calculate the contour levels is modified from
HPDregionplot
in the emdbook package by Ben Bolker (https://cran.r-project.org/package=emdbook). oldstyle = TRUE
-
This style was used for the historical (2017) vignettes, which have been moved to the ‘extdata/cpcp’ directory in JMDplots (https://github.com/jedick/JMDplots). For each dataset, the point symbol is a filled square if the p-values of both the x-variable and y-variable are less than 0.05, a filled circle if the p-value of one of the x- or y-variables is less than 0.05, and an open circle otherwise. A solid line is drawn from the point to the corresponding axis if the rounded, absolute value of (
CLES
in percent - 50) of the x- or y-variable is greater than or equal 10. Otherwise, a dashed line is drawn from the point to the corresponding axis if the p-value of the x- or y-variable is less than 0.05. Otherwise, no line is drawn.
See Also
qdist
to plot quantile distributions for a single dataset.
Examples
library(CHNOSZ)
# Make an old-style plot for two datasets
comptab <- lapply(c("JKMF10", "WDO+15_C.N"), function(dataset) {
pdat <- pdat_colorectal(dataset)
get_comptab(pdat, oldstyle = TRUE)
})
diffplot(comptab, oldstyle = TRUE)