plot.ratio_fit {CalciOMatic} | R Documentation |
The function plot.ratio_fit
performs different kinds of
predefined plots for objects of class ratio_fit
## S3 method for class 'ratio_fit': plot(x, y = NULL, items = 1:5, col = "black", col2 = "darkgray", main = "Intracellular calcium transient: Ratiometric fit", xlabs = c("Time (s)", "Time (s)", "Lag", "Theoretical quant.", "Residuals"), ylabs = c(expression(paste("[", Ca^{2+phantom()}, "] (", mu, "M)")), expression(res[Ca]), "ACF", "Sample quant.", "Counts"), labs = c(expression(A[1]), expression(A[2]), "B", "C", "D"), ylas = 1, ask = FALSE, ...)
x |
an object of class ratio_fit , as returned by
the ratioFitFromDf function |
y |
argument not used (NULL by default) |
items |
a vector of integers (between 1 and 5), telling which plots to draw |
col |
the color of the main signals to plot (either an integer or a character string) |
col2 |
the color of the secondary signals to plot (either an integer or a character string) |
main |
a character string specifying the main title of the figure |
xlabs |
a vector of character strings specifying the label of the x-axes |
ylabs |
a vector of character strings specifying the label of the y-axes |
labs |
a vector of character strings specifying the label at the top-left of each panel (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) |
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" |
If the user does not want to draw all plots in the same figure, (s)he
can set to logical ask
value to TRUE
. In that case,
three symbols (left arrow, black square and right arrow) will be added
at the bottom right of the plot, allowing user interactions. By
clicking on the arrowhead oriented left (resp. right), the user will
draw the previous (resp. next) plot (within items
). By clicking
on the black square, the user will stay on the current plot and none
of the symbols will be available anymore
This plot method does not return anything else that the plotted figures
Sebastien Joucla sebastien.joucla@parisdescartes.fr
plotCalciOMatic
,
plot.fluo_rawdata
,
plot.direct_fit
,
plot.ratio_fit_list
## Load the data from cockroach olfactory interneurons
data(inVitro)
## 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)
## Create the data frame containing the physiological data
## (experiment #2, stimulation #2)
## G and s_ro are the respectively the gain of the CCD camera
## and the standard deviation of its read-out process
physioData <- ratioExpPhysio(dataset="inVitro",
expe=2, stim=2,
idxOn=10,
R_min=R_min, R_max=R_max,
K_eff=K_eff, K_d=K_d,
G=0.146, s_ro=16.4,
alphamethod=FALSE)
## Perform a ratiometric fit
physioRatioFit <- ratioFitFromDf(df = physioData,
transients = 2,
AfterPeak = 14)
## Print the class of 'physioRatioFit'
print(class(physioRatioFit))
## Create the data frame containing the physiological data
## (experiment #2, stimulation #2)
## G and s_ro are the respectively the gain of the CCD camera
## and the standard deviation of its read-out process
physioData <- ratioExpPhysio(dataset="inVitro",
expe=2, stim=2,
idxOn=10,
R_min=R_min, R_max=R_max,
K_eff=K_eff, K_d=K_d,
G=0.146, s_ro=16.4,
alphamethod=FALSE)
## Perform a ratiometric fit using "optim"
physioRatioFit <- ratioFitFromDf(df = physioData,
transients = 2,
AfterPeak = 14)
## Plot the results on the same figure
plot(x=physioRatioFit, items=1:4)
## Plot the results on separate figures and wait for a user action
## plot(x=physioRatioFit, items=1:4, ask=TRUE)