src/Cal_plotting_methods.R

In DmitryMarkovich/Thrombin_Analyzer: Thrombin Analyzer

################################################################################
Cal$set(
    which = "public", name = "plot",
    value = compiler::cmpfun(
        f = function() {
            if (length(data) != 0) {
                ## mar = c(bottom, right, up, left), mgp = c(?, tick values, ticks)
                par(mar = c(4, 7, 2, 0.5), mgp = c(10, 1, 0)); options(scipen = -2);
                graphics::plot(data, axes = FALSE, xlab = NA, ylab = NA,
                               cex = 1.25, lwd = 2, ylim = c(0, max(data$y)));
                grid(nx = NULL, ny = NULL, lty = 2, col = "black", lwd = 1);
                box();
                axis(side = 1, tck = -0.025, labels = NA);
                axis(side = 1, lwd = 0, line = 0.15, cex.axis = 1.5);
                title(xlab = "time, min", line = 2.25, cex.lab = 1.5);
                axis(side = 2, tck = -0.025, labels = NA, col = "black");
                axis(side = 2, lwd = 0, line = -0.4, las = 1, cex.axis = 1.5);
                title(ylab = "Fluorescence, a.u.", line = 5.5, cex.lab = 1.5);
                title(main = "Calibration signal", line = 0.5, cex.main = 1.5);
                ## mtext(text = as.character(signif(num.smry$rat$x, 3)), side = 1,
                ##       line = -1.5, cex = 1.5);
                ## mtext(text = as.character(signif(num.smry$rat$y, 3)), side = 3,
                ##       line = -1.5, cex = 1.5);
            } else {
                warning(">> Cal$data == NULL!");
            }
        }, options = kCmpFunOptions),
    overwrite = FALSE);  ## End of Cal$plot
################################################################################

################################################################################
Cal$set(
    which = "public", name = "plot_fit",
    value = compiler::cmpfun(
        f = function(cal.model) {
            plot();
            lines(data$x, get_model(cal.model), col = "red", lwd = 3);
            if (any(
                cal.model == c("T0LateMM", "LateMM", "T0LateExp", "LateExp")) ||
                (!is.null(fit$Auto_model) &&
                     any(fit$Auto_model ==
                             c("T0LateMM", "LateMM", "T0LateExp", "LateExp")))) {
                lines(data$x, get_init_rate(cal.model), col = "red", lwd = 3, lty = 2);
                legend("bottomright", legend = c("Initial rate"), pch = c(NA),
                       lty = c(2), seg.len = 2.0, lwd = 4, col = c("red"), bg = "white",
                       bty = "y", cex = 1.25);
            }
            if (cal.model == "Auto") {
                model.label <- paste0(fit$Auto_model, " fit (A)");
            } else {
                model.label <- paste0(cal.model, " fit");
            }
            legend("topleft",
                   legend = c("Raw data", model.label),
                   pch = c(1, NA, NA), lty = c(NA, 1), seg.len = 0.5, lwd = 4,
                   col = c("black", "red"), bg = "white", bty = "y",
                   cex = 1.25);
        }, options = kCmpFunOptions),
    overwrite = FALSE);  ## End of Cal$plot_fit
################################################################################

################################################################################
Cal$set(
    which = "public", name = "plot_residuals",
    value = compiler::cmpfun(
        f = function(cal.model) {
            resid <- data$y - get_model(cal.model);
            graphics::plot(x = data$x, y = resid, type = "b", pch = 16, lwd = 1,
                           cex.lab = 1.5, cex.axis = 1.5, xlab = "time, min",
                           ylab = "Fluorescence, a.u.");
            ## mar = c(bottom, right, up, left), mgp = c(?, tick values, ticks)
            par(mar = c(4, 6, 2, 0.75), mgp = c(10, 1, 0)); options(scipen = -2);
            graphics::plot(data$x, resid, axes = FALSE, xlab = NA, type = "b",
                           ylab = NA, cex = 1.25, lwd = 2);
            grid(nx = NULL, ny = NULL, lty = 2, col = "black", lwd = 1);
            box();
            axis(side = 1, tck = -0.025, labels = NA);
            axis(side = 1, lwd = 0, line = 0.15, cex.axis = 1.5);
            title(xlab = "time, min", line = 2.25, cex.lab = 1.5);
            axis(side = 2, tck = -0.025, labels = NA, col = "black");
            axis(side = 2, lwd = 0, line = -0.4, las = 1, cex.axis = 1.5);
            title(ylab = "Fluorescence, a.u.", line = 4.5, cex.lab = 1.5);
            title(main = "Residuals of the fit", line = 0.5, cex.main = 1.5);
            if (cal.model != "Auto") {
                abline(h = fit[[cal.model]]$smry$sigma, lwd = 3);
                abline(h = -fit[[cal.model]]$smry$sigma, lwd = 3);
            } else {
                abline(h = fit[[fit$Auto_model]]$smry$sigma, lwd = 3);
                abline(h = -fit[[fit$Auto_model]]$smry$sigma, lwd = 3);
            }
            ## abline(h = fit[[cal.model]]$smry$sigma, lwd = 3);
            ## abline(h = -fit[[cal.model]]$smry$sigma, lwd = 3);
            legend("top", legend = c("Residuals"), pch = c(1), lty = c(NA),
                   seg.len = 0.5, lwd = 4, col = c("black"), bg = "white", bty = "y",
                   cex = 1);
            legend("bottom", legend = c("Residual standard error of the fit"),
                   pch = c(NA), lty = c(1), seg.len = 0.5, lwd = 4, col = c("black"),
                   bg = "white", bty = "y", cex = 1);
        }, options = kCmpFunOptions),
    overwrite = FALSE);  ## End of Cal$plot_residuals
################################################################################

################################################################################
######################################## Legacy RF classes code
################################################################################

## ################################################################################
## Cal.clear <- function() {
##     data <<- data.frame(); num.smry <<- list(); fit <<- list();
##     parms <<- data.frame();
## }  ## End of Cal.clear
## ################################################################################

## ################################################################################
## Cal.plot <- function() {
##     if (length(data) != 0) {
##         ## mar = c(bottom, right, up, left), mgp = c(?, tick values, ticks)
##         par(mar = c(4, 7, 2, 0.5), mgp = c(10, 1, 0)); options(scipen = -2);
##         graphics::plot(data, axes = FALSE, xlab = NA, ylab = NA, cex = 1.25, lwd = 2,
##                        ylim = c(0, max(data$y))
##                        );
##         grid(nx = NULL, ny = NULL, lty = 2, col = "black", lwd = 1);
##         box();
##         axis(side = 1, tck = -0.025, labels = NA);
##         axis(side = 1, lwd = 0, line = 0.15, cex.axis = 1.5);
##         title(xlab = "time, min", line = 2.25, cex.lab = 1.5);
##         axis(side = 2, tck = -0.025, labels = NA, col = "black");
##         axis(side = 2, lwd = 0, line = -0.4, las = 1, cex.axis = 1.5);
##         title(ylab = "Fluorescence, a.u.", line = 5.5, cex.lab = 1.5);
##         title(main = "Calibration signal", line = 0.5, cex.main = 1.5);
##         mtext(text = as.character(signif(num.smry$rat$x, 3)), side = 1, line = -1.5, cex = 1.5);
##         mtext(text = as.character(signif(num.smry$rat$y, 3)), side = 3, line = -1.5, cex = 1.5);
##     } else {
##         warning(">> Cal$data == NULL!");
##     }
## }  ## End of Cal.plot
## ################################################################################

## ################################################################################
## Cal.plot_fit <- function(cal.model) {
##     plot();
##     lines(data$x, get_model(cal.model), col = "red", lwd = 3);
##     if (any(cal.model == c("T0LateMM", "LateMM", "T0LateExp", "LateExp")) ||
##         (!is.null(fit$Auto_model) &&
##              any(fit$Auto_model ==
##                      c("T0LateMM", "LateMM", "T0LateExp", "LateExp")))) {
##         lines(data$x, get_init_rate(cal.model), col = "red", lwd = 3, lty = 2);
##         legend("bottomright", legend = c("Initial rate"), pch = c(NA),
##                lty = c(2), seg.len = 2.0, lwd = 4, col = c("red"), bg = "white",
##                bty = "y", cex = 1.25);
##     }
##     if (cal.model == "Auto") {
##         model.label <- paste0(fit$Auto_model, " fit (A)");
##     } else {
##         model.label <- paste0(cal.model, " fit");
##     }
##     legend("topleft",
##            legend = c("Raw data", model.label),
##            pch = c(1, NA, NA), lty = c(NA, 1), seg.len = 0.5, lwd = 4,
##            col = c("black", "red"), bg = "white", bty = "y",
##            cex = 1.25);
## }  ## End of Cal.plot_fit
## ################################################################################

## ################################################################################
## Cal.plot_residuals <- function(cal.model) {
##     resid <- data$y - get_model(cal.model);
##     graphics::plot(x = data$x, y = resid, type = "b", pch = 16, lwd = 1,
##                    cex.lab = 1.5, cex.axis = 1.5, xlab = "time, min",
##                    ylab = "Fluorescence, a.u.");
##     ## mar = c(bottom, right, up, left), mgp = c(?, tick values, ticks)
##     par(mar = c(4, 6, 2, 0.75), mgp = c(10, 1, 0)); options(scipen = -2);
##     graphics::plot(data$x, resid, axes = FALSE, xlab = NA, type = "b",
##                    ylab = NA, cex = 1.25, lwd = 2);
##     grid(nx = NULL, ny = NULL, lty = 2, col = "black", lwd = 1);
##     box();
##     axis(side = 1, tck = -0.025, labels = NA);
##     axis(side = 1, lwd = 0, line = 0.15, cex.axis = 1.5);
##     title(xlab = "time, min", line = 2.25, cex.lab = 1.5);
##     axis(side = 2, tck = -0.025, labels = NA, col = "black");
##     axis(side = 2, lwd = 0, line = -0.4, las = 1, cex.axis = 1.5);
##     title(ylab = "Fluorescence, a.u.", line = 4.5, cex.lab = 1.5);
##     title(main = "Residuals of the fit", line = 0.5, cex.main = 1.5);
##     if (cal.model != "Auto") {
##         abline(h = fit[[cal.model]]$smry$sigma, lwd = 3);
##         abline(h = -fit[[cal.model]]$smry$sigma, lwd = 3);
##     } else {
##         abline(h = fit[[fit$Auto_model]]$smry$sigma, lwd = 3);
##         abline(h = -fit[[fit$Auto_model]]$smry$sigma, lwd = 3);
##     }
##     ## abline(h = fit[[cal.model]]$smry$sigma, lwd = 3);
##     ## abline(h = -fit[[cal.model]]$smry$sigma, lwd = 3);
##     legend("top", legend = c("Residuals"), pch = c(1), lty = c(NA),
##            seg.len = 0.5, lwd = 4, col = c("black"), bg = "white", bty = "y",
##            cex = 1);
##     legend("bottom", legend = c("Residual standard error of the fit"),
##            pch = c(NA), lty = c(1), seg.len = 0.5, lwd = 4, col = c("black"),
##            bg = "white", bty = "y", cex = 1);
## }  ## End of Cal.plot_residuals
## ################################################################################

################################################################################
######################################## End of Legacy RF classes code
################################################################################