plot.ratio_fit {CalciOMatic}R Documentation

Plot Method for Objects of Class "ratio_fit"

Description

The function plot.ratio_fit performs different kinds of predefined plots for objects of class ratio_fit

Usage

## 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, ...)

Arguments

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"

Details

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

Value

This plot method does not return anything else that the plotted figures

Author(s)

Sebastien Joucla sebastien.joucla@parisdescartes.fr

See Also

plotCalciOMatic, plot.fluo_rawdata, plot.direct_fit, plot.ratio_fit_list

Examples

## 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)

[Package CalciOMatic version 1.1-3 Index]