plot_panel: Plot Panel

Description

The plot_panel function takes objects of the class adpcr to enable customizable graphical representations of a chamber-based digital PCR experiments (e.g., Digital Array (R) IFCs (integrated fluidic circuits) of the BioMark (R) and EP1 (R)).

Usage

plot_panel(input, nx_a, ny_a, col = "red", legend = TRUE, half = "none", ...)

Arguments

input

object of the adpcr class. See Details.

nx_a

Number of columns in a plate.

ny_a

Number of rows in a plate.

col

A single color or vector of colors for each level of input.

legend

If TRUE, a built-in legend is added to the plot.

half

If left or right, every well is represented only by the adequate half of the rectangle.

...

Arguments to be passed to plot function.

Value

A list of coordinates of each microfluidic well and an assigned color.

Details

Currently only objects containing just one column of data (one panel) can be plotted (see Examples how easily plot multipanel objects). Moreover the object must contain fluorescence intensities or exact number of molecules or the positive hits derived from the Cq values for each well. The Cq values can be obtained by custom made functions (see example in dpcr_density)) or the yet to implement "qpcr_analyser function from the dpcR package.

If the col argument has length one, a color is assigned for each interval of the input, with the brightest colors for the lowest values.

Examples

Run this code

# Create a sample dPCR experiment with 765 elements (~> virtual compartments)   
# of target molecule copies per compartment as integer numbers (0,1,2)
ttest <- sim_adpcr(m = 400, n = 765, times = 20, pos_sums = FALSE, 
                   n_panels = 1)
# Plot the dPCR experiment results with default settings
plot_panel(ttest, nx_a = 45, ny_a = 17)

# Apply a binary color code with blue as positive
ttest@breaks <- c(0, 2, 4)
plot_panel(ttest, nx_a = 45, ny_a = 17, col = "blue")

# Apply a two color code for number of copies per compartment
plot_panel(ttest, nx_a = 45, ny_a = 17, col = c("blue", "red"))

# supply customized breaks and compare
par(mfcol = c(2, 1))
plot_panel(ttest, nx_a = 45, ny_a = 17)
slot(ttest, "breaks") <- c(0, 1, 2, (max(slot(ttest, "breaks")) + 1))
plot_panel(ttest, nx_a = 45, ny_a = 17)
par(mfcol = c(1, 1))

# plot few panels
ttest2 <- sim_adpcr(m = 400, n = 765, times = 40, pos_sums = FALSE, 
                    n_panels = 4)
par(mfcol = c(2, 2))
four_panels <- lapply(1:ncol(ttest2), function(i) 
       plot_panel(extract_dpcr(ttest2, i), nx_a = 45, ny_a = 17, legend = FALSE, 
         main = paste("Panel", LETTERS[i], sep = "")))
par(mfcol = c(1, 1))

# two different channels 
plot_panel(extract_dpcr(ttest2, 1), nx_a = 45, ny_a = 17, legend = FALSE, 
           half = "left")
par(new = TRUE)
plot_panel(extract_dpcr(ttest2, 2), nx_a = 45, ny_a = 17, col = "blue", 
           legend = FALSE, half = "right")

# plot two panels with every well as only the half of the rectangle
ttest3 <- sim_adpcr(m = 400, n = 765, times = 40, pos_sums = FALSE, 
                    n_panels = 2)
par(mfcol = c(1, 2))
two_panels <- lapply(1:ncol(ttest3), function(i) 
       plot_panel(extract_dpcr(ttest3, i), nx_a = 45, ny_a = 17, legend = FALSE, 
         main = paste("Panel", LETTERS[i], sep = "")))
par(mfcol = c(1, 1))