Description Usage Arguments Details Plot style See Also Examples
Make a plot showing differences of selected chemical metrics.
1 2 3 4 5 |
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 |
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.
The overall style of the plot is controlled by oldstyle
.
oldstyle = FALSE
This is the current default style.
Use pch
and cex
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) and col.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.
qdist
to plot quantile distributions for a single dataset.
1 2 3 4 5 6 7 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.