plotCalciOMatic {CalciOMatic} | R Documentation |
The low-level function plotCalciOMatic
performs different
kinds of predefined plots, depending on the value of n
. It is
generally called by plot methods dedicated to several types of objects
("fluo_rawdata"
, "ratio_fit"
, "ratio_fit_list"
or
"direct_fit"
)
plotCalciOMatic(x = NULL, y = NULL, n = 1, x2 = NULL, y2 = NULL, col = "black", col2 = "darkgray", main = "MyCalciumRatiometricFit", xlab = "", ylab = "", lab = "A", ylas = 1, oma = c(4, 0, 1, 0), mar = c(0, 7, 2, 0), ask = FALSE, ...)
x |
the abscissa of the main signal to plot (see details below) |
y |
the main signal to plot (see details below) |
n |
an integer, between 1 and 5, telling which kind of plot is used (see details below) |
x2 |
the abscissa of the secondary signal to plot (see details below) |
y2 |
the secondary signal to plot (see details below) |
col |
the color of the main signal (either an integer or a character string) |
col2 |
the color of the secondary signal (either an integer or a character string) |
main |
a character string specifying the main title of the plot |
xlab |
a character string specifying the label of the x-axis |
ylab |
a character string specifying the label of the y-axis |
lab |
a character string specifying the label at the top-left of the plot (generally a letter, a letter with an integer, or an expression) |
ylas |
an integer specifying the orientation of the yticks. Possible values are 0 or 3 (vertical), or 1 or 2 (horizontal) |
oma |
a vector of length 4 specifying the outer margin of the figure |
mar |
a vector of length 4 specifying the margin of the panel to add |
ask |
a logical value. Set to FALSE to draw all plots on
the same figure. If set to TRUE , a single device will be
opened, in which the first plot will be drawn. Three symbols (left
arrow, black square and right arrow) will be added at the bottom
right of the plot, for interactions with the user (see details
below) |
... |
one or more of the following plot parameters:
"cex" , "cex.axis" , "cex.lab" ,
"cex.main" , "font" , "font.axis" ,
"font.lab" , "font.main" , "line.xlab" ,
"line.ylab" , "line.lab" , "line.main" ,
"adj.main" , "xlim" , "ylim" , "tcl" ,
"mgp.x" , "mgp.y" |
The third argument of the plot.calciomatic
function is an
integer n
comprised between 1 and 5. The plot drawn directly
depends on the value of n
, as follows:
n=1
y
vs. x
(type lines
and
color col
), and superimpose the plot of
y2
vs. x2
(color col2
). Used to
plot raw data and fitted data vs. time valuesn=2
y
vs. x
(type lines
and
color col
), and add a dashed horizontal line
at y=0 (color col2
). Used to plot fit
residualsn=3
y
of class "acf"
(color col
), and add a 95%
confidence band between
y= - 1.96 /sqrt(length(y$acf))
and
y= + 1.96 /sqrt(length(y$acf))
(color col2
). Used to plot the
auto-correlation function of the residualsn=4
y
vs. x
(type points
and
color col
), add a diagonal dashed line
(color col
) and a 95%
confidence band (color col2
). Used to plot
quantile-quantile plots of the fit residualsn=5
x
(color col
),
and add vertical dashed lines at -3/-2/-1/0/1/2/3
times the standard deviation of x
(color
col2
). Used to plot the histogram of the fit
residuals
When ask
is set to its default FALSE
value, a plot is
drawn, and nothing else is returned by the function. If ask
is
set to TRUE
, the action to execute is returned, as a character
string
Sebastien Joucla sebastien.joucla@parisdescartes.fr
plot.fluo_rawdata
,
plot.ratio_fit
,
plot.ratio_fit_list
,
plot.direct_fit
## Plot simulated fluorescence raw data. A simpler way would be to ## use the high-level plot.fluo_rawdata function, so, this example ## is just for the sake of the form ## Parameters of the monoexponential calcium transient tOn <- 1 Time <- seq(0,12,length.out=160) Ca0 <- 0.10 dCa <- 0.25 tau <- 1.5 ## Calibrated parameters R_min <- list(value=0.136, mean=0.136, se=0.00363, USE_se=TRUE) R_max <- list(value=2.701, mean=2.701, se=0.151, USE_se=TRUE) K_eff <- list(value=3.637, mean=3.637, se=0.729, USE_se=TRUE) K_d <- list(value=0.583, mean=0.583, se=0.123, USE_se=TRUE) ## Experiment-specific parameters nb_B <- 1 B_T <- 100.0 T_340 <- 0.015 T_380 <- 0.006 P <- 200 P_B <- 200 phi <- 2 S_B_340 <- 30 S_B_380 <- 80 ## Create a monoexponential calcium decay Ca <- caMonoExp(t = Time, tOn = tOn, Ca0 = Ca0, dCa = dCa, tau = tau) ## Simulate the corresponding ratiometric experiment df <- ratioExpSimul(nb_B = nb_B, Ca = Ca, R_min = R_min, R_max = R_max, K_eff = K_eff, K_d = K_d, B_T = B_T, phi = phi, S_B_340 = S_B_340, S_B_380 = S_B_380, T_340 = T_340, T_380 = T_380, P = P, P_B = P_B, ntransients = 1, G = 1, s_ro = 0) ## Extract relevant data from the data frame Time <- with(df,Time[!is.na(Time) & lambda==340]) adu_340 <- with(df,adu[!is.na(Time) & lambda==340]) adu_380 <- with(df,adu[!is.na(Time) & lambda==380]) ## Plot the fluorescence data in the same figure par(oma = c(4, 0, 1, 0), mar = c(0, 7, 2, 0)) layout(matrix(c(1,2),ncol=1)) plotCalciOMatic(x = Time, y = adu_340, n = 1, xlab = "", ylab = expression(paste(adu[340], "(photons)")), lab = "A", main = "Fluorescence Raw Data") plotCalciOMatic(x = Time, y = adu_380, n = 1, xlab = "Time (s)", ylab = expression(paste(adu[380], " (photons)")), lab = "B", main = "")