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## normfluodbf - R package that Cleans and Normalizes FLUOstar DBF and DAT Files
## Copyright (C) 2024 Tingwei Adeck
#' Plot Plate - Favorite is Fluostar style
#' @family normfluodbfplots
#' @param x plot requirement
#' @param whichplot int
#' @param fluorstarplot whichplot = 1
#' @param superimpose whichplot = 2
#' @param plate_layout whichplot = 3
#' @param plot_side_by_side whichplot = 4
#' @param legend_labels labels whichplot = 2,4
#' @param plot_name plot name
#' @param ... additional parameters
#' @return plot object
#' @name normfluodbfplots
#' @examples
#' \dontrun{plot(plate, whichplot = 1)}
NULL
#' @rdname normfluodbfplots
#' @return print plot (return plate)
#' @export
plot.96well_plate = function(x,
whichplot = 1,
fluorstarplot = 1 %in% whichplot,
superimpose = 2 %in% whichplot,
plate_layout = 3 %in% whichplot,
plot_side_by_side = 4 %in% whichplot,
legend_labels = NULL,
plot_name = NULL,
...){
plate <- x
plt.obj <- plot_canvas(plate)
data <- subset_or_not(plate)
title <- sprintf('%s vs %s',y_var(plate),x_var_two_label(plate))
ylab <- params(plate, 'GENERAL', 'Y_VAR')
if (is.null(whichplot) || is.null(fluorstarplot) || fluorstarplot){
plt.obj <- plot_grid(data, plt.obj)
plt.obj <- plot_in_well(plt.obj, data, no_annotations = F)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'fluostar_plot'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.obj
print(plt.obj)
invisible(plate)
}
else if (superimpose){
plot_superimpose_advanced(data = data,
plt.obj = plt.obj,
legend_labels = legend_labels)
plate <- remove_legend(plate)
plate <- remove_subset_data(plate)
invisible(plate)
}
else if (plate_layout){
plt.layout <- plot_plate_layout(plate)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'plate_layout'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.layout
invisible(plate)
}
else if (plot_side_by_side){
plt <- plot_side_by_side(data = data,
plt.obj = plt.obj,
ylab = ylab,
title = title,
legend_labels = legend_labels)
plate <- remove_subset_data(plate)
invisible(plate)
}
else {
plt.obj <- plot_grid(data, plt.obj)
plt.obj <- plot_in_well(plt.obj, data, no_annotations = F)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'fluostar_plot'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.obj
print(plt.obj)
invisible(plate)
}
}
#' @rdname normfluodbfplots
#' @return print plot (return plate)
#' @export
plot.384well_plate = function(x,
whichplot = 1,
fluorstarplot = 1 %in% whichplot,
superimpose = 2 %in% whichplot,
plate_layout = 3 %in% whichplot,
plot_side_by_side = 4 %in% whichplot,
legend_labels = NULL,
plot_name = NULL,
...){
plate <- x
plt.obj <- plot_canvas(plate)
data <- subset_or_not(plate)
title <- sprintf('%s vs %s',y_var(plate),x_var_two_label(plate))
ylab <- params(plate, 'GENERAL', 'Y_VAR')
if (is.null(whichplot) || is.null(fluorstarplot) || fluorstarplot){
plt.obj <- plot_grid(data, plt.obj)
plt.obj <- plot_in_well(plt.obj, data, no_annotations = F)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'fluostar_plot'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.obj
print(plt.obj)
invisible(plate)
}
else if (superimpose){
plot_superimpose_advanced(data = data,
plt.obj = plt.obj,
legend_labels = legend_labels)
plate <- remove_legend(plate)
plate <- remove_subset_data(plate)
invisible(plate)
}
else if (plate_layout){
plt.layout <- plot_plate_layout(plate)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'plate_layout'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.layout
invisible(plate)
}
else if (plot_side_by_side){
plt <- plot_side_by_side(data = data,
plt.obj = plt.obj,
ylab = ylab,
title = title,
legend_labels = legend_labels)
plate <- remove_subset_data(plate)
invisible(plate)
}
else {
plt.obj <- plot_grid(data, plt.obj)
plt.obj <- plot_in_well(plt.obj, data, no_annotations = F)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'fluostar_plot'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.obj
print(plt.obj)
invisible(plate)
}
}
#' @rdname normfluodbfplots
#' @return print plot (return plate)
#' @export
plot.1536well_plate_t1 = function(x,
whichplot = 1,
fluorstarplot = 1 %in% whichplot,
superimpose = 2 %in% whichplot,
plate_layout = 3 %in% whichplot,
plot_side_by_side = 4 %in% whichplot,
legend_labels = NULL,
plot_name = NULL,
...){
plate <- x
plt.obj <- plot_canvas(plate)
data <- subset_or_not(plate)
title <- sprintf('%s vs %s',y_var(plate),x_var_two_label(plate))
ylab <- params(plate, 'GENERAL', 'Y_VAR')
if (is.null(whichplot) || is.null(fluorstarplot) || fluorstarplot){
plt.obj <- plot_grid(data, plt.obj)
plt.obj <- plot_in_well(plt.obj, data, no_annotations = F)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'fluostar_plot'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.obj
print(plt.obj)
invisible(plate)
}
else if (superimpose){
plot_superimpose_advanced(data = data,
plt.obj = plt.obj,
legend_labels = legend_labels)
plate <- remove_legend(plate)
plate <- remove_subset_data(plate)
invisible(plate)
}
else if (plate_layout){
plt.layout <- plot_plate_layout(plate)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'plate_layout'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.layout
invisible(plate)
}
else if (plot_side_by_side){
plt <- plot_side_by_side(data = data,
plt.obj = plt.obj,
ylab = ylab,
title = title,
legend_labels = legend_labels)
plate <- remove_subset_data(plate)
invisible(plate)
}
else {
plt.obj <- plot_grid(data, plt.obj)
plt.obj <- plot_in_well(plt.obj, data, no_annotations = F)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'fluostar_plot'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.obj
print(plt.obj)
invisible(plate)
}
}
#' @rdname normfluodbfplots
#' @return print plot (return plate)
#' @export
plot.1536well_plate_t2 = function(x,
whichplot = 1,
fluorstarplot = 1 %in% whichplot,
superimpose = 2 %in% whichplot,
plate_layout = 3 %in% whichplot,
plot_side_by_side = 4 %in% whichplot,
legend_labels = NULL,
plot_name = NULL,
...){
plate <- x
plt.obj <- plot_canvas(plate)
data <- subset_or_not(plate)
title <- sprintf('%s vs %s',y_var(plate),x_var_two_label(plate))
ylab <- params(plate, 'GENERAL', 'Y_VAR')
if (is.null(whichplot) || is.null(fluorstarplot) || fluorstarplot){
plt.obj <- plot_grid(data, plt.obj)
plt.obj <- plot_in_well(plt.obj, data, no_annotations = F)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'fluostar_plot'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.obj
print(plt.obj)
invisible(plate)
}
else if (superimpose){
plot_superimpose(data = data,
ylab = ylab,
title = title,
legend_labels = legend_labels)
plate <- remove_legend(plate)
plate <- remove_subset_data(plate)
invisible(plate)
}
else if (plate_layout){
plt.layout <- plot_plate_layout(plate)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'plate_layout'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.layout
invisible(plate)
}
else if (plot_side_by_side){
plt <- plot_side_by_side(data = data,
plt.obj = plt.obj,
ylab = ylab,
title = title,
legend_labels = legend_labels)
plate <- remove_subset_data(plate)
invisible(plate)
}
else {
plt.obj <- plot_grid(data, plt.obj)
plt.obj <- plot_in_well(plt.obj, data, no_annotations = F)
plate <- remove_subset_data(plate)
if (is.null(plot_name))
plot_name <- 'fluostar_plot'
else
plot_name <- plot_name
plate[[plot_name]] <- plt.obj
print(plt.obj)
invisible(plate)
}
}
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