In michbur/HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data
Report generated on r Sys.time() using the HaDeX R package.
Detected input file: r ifelse(is.null(input[["data_file"]][["name"]]), "none", input[["data_file"]][["name"]]).
MD5 hash of the input file: r ifelse(is.null(input[["data_file"]][["name"]]), "none (example file)", tools::md5sum(as.character(input[["data_file"]][["datapath"]]))).
Summary
Protein name : r as.character(unique(dat()[["Protein"]]))
Protein sequence : r protein_sequence_colored()
Sequence length : r input[["sequence_length"]]
knitr::kable(summary_data())
if (input[["export_overlap_dist"]]){
cat("## Overlap Distribution \n")
stateOverlapDist()
}
if (input[["export_overlap_dist_data"]]){
cat("## Overlap Distribution Data \n")
stateOverlapDist_data()
}
if (input[["export_overlap_graph"]]){
cat("## Overlap Graphically \n")
stateOverlap_out()
}
if (input[["export_overlap_graph_data"]]){
cat("## Overlap Graphically Data \n")
stateOverlap_data()
}
if (input[["export_comparison_plot"]]){
cat("## Comparison Plot \n")
cat("### Relative values \n")
if(has_modifications()){
cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.")
} else{
if(input[["out_time"]] == 99999){
cat(paste0("Chosen control: ", input[["chosen_control"]], "."))
} else{
cat("No chosen control. \n")
}
}
p <- comparison_plot_exp() +
scale_color_manual(values = as.vector(comparison_plot_colors_chosen()))
if(!input[["theory"]] & input[["calc_type"]]=="relative"){
p +
coord_cartesian(ylim = c(input[["comp_plot_y_range"]][[1]], input[["comp_plot_y_range"]][[2]]),
xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = input[["comparison_plot_title"]],
x = input[["comparison_plot_x_label"]],
y = input[["comparison_plot_y_label"]])
} else {
p +
coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = paste0("Fraction exchanged in state comparison in ", input[["chosen_time"]], " min"),
x = "Position in sequence",
y = "Fraction exchanged [%]")
}
}
if (input[["export_comparison_plot"]]){
cat("### Absolute values \n")
p <- comparison_plot_exp_abs() +
scale_color_manual(values = as.vector(comparison_plot_colors_chosen()))
if (!input[["theory"]] & input[["calc_type"]]=="absolute"){
p +
coord_cartesian(ylim = c(input[["comp_plot_y_range"]][[1]], input[["comp_plot_y_range"]][[2]]),
xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = input[["comparison_plot_title"]],
x = input[["comparison_plot_x_label"]],
y = input[["comparison_plot_y_label"]])
} else {
p +
coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = paste0("Absolute value exchanged in state comparison in ", input[["chosen_time"]], " min"),
x = "Position in sequence",
y = "Absolute value exchanged [Da]")
}
}
if (input[["export_comparison_plot_data"]]){
cat("## Comparison Plot Data \n")
cat("### Relative values \n")
if(has_modifications()){
cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.")
} else{
if(input[["out_time"]] == 99999){
cat(paste0("Chosen control: ", input[["chosen_control"]], "."))
} else{
cat("No chosen control. \n")
}
}
comparison_plot_data_exp()
}
if (input[["export_comparison_plot_data"]]){
cat("### Absolute values \n")
comparison_plot_data_exp_abs()
}
if (input[["export_theo_comparison_plot"]]){
cat("## Theoretical Comparison Plot \n")
cat("### Relative values \n")
cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%."))
p <- comparison_plot_theo() +
scale_color_manual(values = as.vector(comparison_plot_colors_chosen()))
if(input[["theory"]] & input[["calc_type"]]=="relative"){
p +
coord_cartesian(ylim = c(input[["comp_plot_y_range"]][[1]], input[["comp_plot_y_range"]][[2]]),
xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = input[["comparison_plot_title"]],
x = input[["comparison_plot_x_label"]],
y = input[["comparison_plot_y_label"]])
} else {
p +
coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = paste0("Theoretical fraction exchanged in state comparison in ", input[["chosen_time"]], " min"),
x = "Position in sequence",
y = "Theoretical fraction exchanged [%]")
}
}
if (input[["export_theo_comparison_plot"]]){
cat("### Absolute values \n")
p <- comparison_plot_theo_abs() +
scale_color_manual(values = as.vector(comparison_plot_colors_chosen()))
if(input[["theory"]] & input[["calc_type"]]=="absolute"){
p +
coord_cartesian(ylim = c(input[["comp_plot_y_range"]][[1]], input[["comp_plot_y_range"]][[2]]),
xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = input[["comparison_plot_title"]],
x = input[["comparison_plot_x_label"]],
y = input[["comparison_plot_y_label"]])
} else {
p +
coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]]))+
labs(title = paste0("Theoretical absolute value exchanged in state comparison in ", input[["chosen_time"]], " min"),
x = "Position in sequence",
y = "Theoretical absolute value exchanged [Da]")
}
}
if (input[["export_theo_comparison_plot_data"]]){
cat("## Theoretical Comparison Plot Data \n")
cat("### Relative values \n")
cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%."))
comparison_plot_data_theo()
}
if (input[["export_theo_comparison_plot_data"]]){
cat("### Absolute values \n")
comparison_plot_data_theo_abs()
}
if (input[["export_woods_plot"]]){
cat("## Woods Plot \n")
cat("### Relative values \n")
if(has_modifications()){
cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.")
} else{
if(input[["out_time"]] == 99999){
cat(paste0("Chosen control: ", input[["chosen_control"]], "."))
} else{
cat("No chosen control. \n")
}
}
p <- differential_plot_exp()
if(!input[["theory"]] & input[["calc_type"]] == "relative"){
p +
coord_cartesian(ylim = c(input[["woods_plot_y_range"]][[1]], input[["woods_plot_y_range"]][[2]]),
xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = input[["woods_plot_title"]],
x = input[["woods_plot_x_label"]],
y = input[["woods_plot_y_label"]])
} else {
p +
coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = paste0("Delta Fraction exchanged in ", input[["chosen_time"]], " min between ", gsub("_", " ", input[["state_first"]]), " and ", gsub("_", " ", input[["state_second"]])),
x = "Position in sequence",
y = "Delta Fraction exchanged between states [%]")
}
}
if (input[["export_woods_plot"]]){
cat("### Absolute values \n")
p <- differential_plot_exp_abs()
if(!input[["theory"]] & input[["calc_type"]] == "absolute"){
p +
coord_cartesian(ylim = c(input[["woods_plot_y_range"]][[1]], input[["woods_plot_y_range"]][[2]]),
xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = input[["woods_plot_title"]],
x = input[["woods_plot_x_label"]],
y = input[["woods_plot_y_label"]])
} else {
p +
coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = paste0("Delta Fraction exchanged in ", input[["chosen_time"]], " min between ", gsub("_", " ", input[["state_first"]]), " and ", gsub("_", " ", input[["state_second"]])),
x = "Position in sequence",
y = "Delta Absolute value exchanged between states [Da]")
}
}
if (input[["export_woods_plot_data"]]){
cat("## Woods Plot Data \n")
cat("### Relative values \n")
if(has_modifications()){
cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.")
} else{
if(input[["out_time"]] == 99999){
cat(paste0("Chosen control: ", input[["chosen_control"]], "."))
} else{
cat("No chosen control. \n")
}
}
differential_plot_data_exp()
}
if (input[["export_woods_plot_data"]]){
cat("### Absolute values \n")
differential_plot_data_exp_abs()
}
if (input[["export_theo_woods_plot"]]){
cat("## Theoretical Woods Plot \n")
cat("### Relative values \n")
cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%."))
p <- differential_plot_theo()
if(input[["theory"]] & input[["calc_type"]] == "relative"){
p +
coord_cartesian(ylim = c(input[["woods_plot_y_range"]][[1]], input[["woods_plot_y_range"]][[2]]),
xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = input[["woods_plot_title"]],
x = input[["woods_plot_x_label"]],
y = input[["woods_plot_y_label"]])
} else {
p +
coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = paste0("Delta Theoretical fraction exchanged in ", input[["chosen_time"]], " min between ", gsub("_", " ", input[["state_first"]]), " and ", gsub("_", " ", input[["state_second"]])),
x = "Position in sequence",
y = "Delta Theoretical fraction exchanged between states [%]")
}
}
if (input[["export_theo_woods_plot"]]){
cat("### Absolute values \n")
p <- differential_plot_theo_abs()
if(input[["theory"]] & input[["calc_type"]] == "absolute"){
p +
coord_cartesian(ylim = c(input[["woods_plot_y_range"]][[1]], input[["woods_plot_y_range"]][[2]]),
xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = input[["woods_plot_title"]],
x = input[["woods_plot_x_label"]],
y = input[["woods_plot_y_label"]])
} else {
p +
coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) +
labs(title = paste0("Delta Theoretical fraction exchanged in ", input[["chosen_time"]], " min between ", gsub("_", " ", input[["state_first"]]), " and ", gsub("_", " ", input[["state_second"]])),
x = "Position in sequence",
y = "Delta Theoretical absoute value exchanged between states [Da]")
}
}
if (input[["export_theo_woods_plot_data"]]){
cat("## Theoretical Woods Plot Data \n")
cat("### Relative values \n")
cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%."))
differential_plot_data_theo()
}
if (input[["export_theo_woods_plot_data"]]){
cat("### Absolute values \n")
differential_plot_data_theo_abs()
}
kin_valid <- length(input[["peptide_list_data_rows_selected"]]) > 0
if (input[["export_kin_plot"]]){
cat("## Uptake curve \n")
if (kin_valid) {
cat("### Relative values \n")
if(has_modifications()){
cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.")
} else{
if(input[["out_time"]] == 99999){
cat(paste0("Chosen control: ", input[["chosen_control"]], "."))
} else{
cat("No chosen control. \n")
}
}
p <- kin_plot_exp()
if(!input[["theory"]] & input[["calc_type"]]=="relative"){
p +
coord_cartesian(ylim = c(input[["kin_plot_y_range"]][[1]], input[["kin_plot_y_range"]][[2]])) +
labs(title = input[["kin_plot_title"]],
x = input[["kin_plot_x_label"]],
y = input[["kin_plot_y_label"]]) +
theme(legend.position = "bottom",
legend.title = element_blank())
} else {
p +
labs(title = "Uptake curve for chosen peptides",
x = "Time points [min]",
y = "Deuteration [%]") +
scale_y_continuous(limits = c(0, 110)) +
theme(legend.position = "bottom",
legend.title = element_blank())
}
} else {
"Uptake curve cannot be shown - no peptides were selected"
}
}
if (input[["export_kin_plot"]]){
if (kin_valid) {
cat("### Absolute values \n")
p <- kin_plot_exp_abs()
if (!input[["theory"]] & input[["calc_type"]]=="absolute"){
p +
coord_cartesian(ylim = c(input[["kin_plot_y_range"]][[1]], input[["kin_plot_y_range"]][[2]])) +
labs(title = input[["kin_plot_title"]],
x = input[["kin_plot_x_label"]],
y = input[["kin_plot_y_label"]]) +
theme(legend.position = "bottom",
legend.title = element_blank())
} else {
p +
labs(title = "Uptake curve for chosen peptides",
x = "Time points [min]",
y = "Deuteration [Da]") +
scale_y_continuous(limits = c(0, NA)) +
theme(legend.position = "bottom",
legend.title = element_blank())
}
}
}
if (input[["export_kin_plot_data"]]){
cat("## Uptake curve Data \n")
if (kin_valid){
cat("### Relative values \n")
if(has_modifications()){
cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.")
} else{
if(input[["out_time"]] == 99999){
cat(paste0("Chosen control: ", input[["chosen_control"]], "."))
} else{
cat("No chosen control. \n")
}
}
kin_plot_exp_data()
} else {
"Uptake curve data cannot be shown - no peptides were selected"
}
}
if (input[["export_kin_plot_data"]]){
if (kin_valid) {
cat("### Absolute values \n")
kin_plot_exp_abs_data()
}
}
if (input[["export_theo_kin_plot"]]){
cat("## Theoretical Uptake curve Data \n")
if (kin_valid){
cat("### Relative values \n")
cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%."))
p <- kin_plot_theo()
if(input[["theory"]] & input[["calc_type"]]=="relative"){
p +
coord_cartesian(ylim = c(input[["kin_plot_y_range"]][[1]], input[["kin_plot_y_range"]][[2]])) +
labs(title = input[["kin_plot_title"]],
x = input[["kin_plot_x_label"]],
y = input[["kin_plot_y_label"]]) +
theme(legend.position = "bottom",
legend.title = element_blank())
} else {
p +
labs(title = "Theoretical uptake curve for chosen peptides",
x = "Time points [min]",
y = "Deuteration [%]") +
scale_y_continuous(limits = c(0, 110)) +
theme(legend.position = "bottom",
legend.title = element_blank())
}
} else {
"Theoretical uptake curve plot cannot be shown - no peptides were selected"
}
}
if (input[["export_theo_kin_plot"]]){
if (kin_valid) {
cat("### Absolute values \n")
p <- kin_plot_theo_abs()
if(input[["theory"]] & input[["calc_type"]]=="absolute"){
p +
coord_cartesian(ylim = c(input[["kin_plot_y_range"]][[1]], input[["kin_plot_y_range"]][[2]])) +
labs(title = input[["kin_plot_title"]],
x = input[["kin_plot_x_label"]],
y = input[["kin_plot_y_label"]]) +
theme(legend.position = "bottom",
legend.title = element_blank())
} else {
p +
labs(title = "Theoretical uptake curve for chosen peptides",
x = "Time points [min]",
y = "Deuteration [Da]") +
scale_y_continuous(limits = c(0, NA)) +
theme(legend.position = "bottom",
legend.title = element_blank())
}
}
}
if (input[["export_theo_kin_plot_data"]]){
cat("## Theoretical uptake curve Data \n")
if (kin_valid){
cat("### Relative values \n")
cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%."))
kin_plot_theo_data()
} else {
"Theoretical uptake curve data cannot be shown - no peptides were selected"
}
}
if (input[["export_theo_kin_plot_data"]]){
if (kin_valid){
cat("### Absolute values \n")
kin_plot_theo_abs_data()
}
}
if (input[["export_quality_control_plot"]]){
cat("## Quality Control Plot \n")
cat("Quality control plot is based purely on experimental values.")
qc_out()
}
if (input[["export_quality_control_plot_data"]]){
cat("## Quality Control Plot Data \n")
cat("Quality control plot data is based purely on experimental values.")
quality_control_plot_data_out()
}
R Session
pander::pander(sessionInfo())
michbur/HaDeX documentation built on March 29, 2022, 5:46 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Report generated on r Sys.time() using the HaDeX R package.
Detected input file: r ifelse(is.null(input[["data_file"]][["name"]]), "none", input[["data_file"]][["name"]]).
MD5 hash of the input file: r ifelse(is.null(input[["data_file"]][["name"]]), "none (example file)", tools::md5sum(as.character(input[["data_file"]][["datapath"]]))).
Summary
Protein name : r as.character(unique(dat()[["Protein"]]))
Protein sequence : r protein_sequence_colored()
Sequence length : r input[["sequence_length"]]
knitr::kable(summary_data())
if (input[["export_overlap_dist"]]){ cat("## Overlap Distribution \n") stateOverlapDist() }
if (input[["export_overlap_dist_data"]]){ cat("## Overlap Distribution Data \n") stateOverlapDist_data() }
if (input[["export_overlap_graph"]]){ cat("## Overlap Graphically \n") stateOverlap_out() }
if (input[["export_overlap_graph_data"]]){ cat("## Overlap Graphically Data \n") stateOverlap_data() }
if (input[["export_comparison_plot"]]){ cat("## Comparison Plot \n") cat("### Relative values \n") if(has_modifications()){ cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.") } else{ if(input[["out_time"]] == 99999){ cat(paste0("Chosen control: ", input[["chosen_control"]], ".")) } else{ cat("No chosen control. \n") } } p <- comparison_plot_exp() + scale_color_manual(values = as.vector(comparison_plot_colors_chosen())) if(!input[["theory"]] & input[["calc_type"]]=="relative"){ p + coord_cartesian(ylim = c(input[["comp_plot_y_range"]][[1]], input[["comp_plot_y_range"]][[2]]), xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = input[["comparison_plot_title"]], x = input[["comparison_plot_x_label"]], y = input[["comparison_plot_y_label"]]) } else { p + coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = paste0("Fraction exchanged in state comparison in ", input[["chosen_time"]], " min"), x = "Position in sequence", y = "Fraction exchanged [%]") } }
if (input[["export_comparison_plot"]]){ cat("### Absolute values \n") p <- comparison_plot_exp_abs() + scale_color_manual(values = as.vector(comparison_plot_colors_chosen())) if (!input[["theory"]] & input[["calc_type"]]=="absolute"){ p + coord_cartesian(ylim = c(input[["comp_plot_y_range"]][[1]], input[["comp_plot_y_range"]][[2]]), xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = input[["comparison_plot_title"]], x = input[["comparison_plot_x_label"]], y = input[["comparison_plot_y_label"]]) } else { p + coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = paste0("Absolute value exchanged in state comparison in ", input[["chosen_time"]], " min"), x = "Position in sequence", y = "Absolute value exchanged [Da]") } }
if (input[["export_comparison_plot_data"]]){ cat("## Comparison Plot Data \n") cat("### Relative values \n") if(has_modifications()){ cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.") } else{ if(input[["out_time"]] == 99999){ cat(paste0("Chosen control: ", input[["chosen_control"]], ".")) } else{ cat("No chosen control. \n") } } comparison_plot_data_exp() }
if (input[["export_comparison_plot_data"]]){ cat("### Absolute values \n") comparison_plot_data_exp_abs() }
if (input[["export_theo_comparison_plot"]]){ cat("## Theoretical Comparison Plot \n") cat("### Relative values \n") cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%.")) p <- comparison_plot_theo() + scale_color_manual(values = as.vector(comparison_plot_colors_chosen())) if(input[["theory"]] & input[["calc_type"]]=="relative"){ p + coord_cartesian(ylim = c(input[["comp_plot_y_range"]][[1]], input[["comp_plot_y_range"]][[2]]), xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = input[["comparison_plot_title"]], x = input[["comparison_plot_x_label"]], y = input[["comparison_plot_y_label"]]) } else { p + coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = paste0("Theoretical fraction exchanged in state comparison in ", input[["chosen_time"]], " min"), x = "Position in sequence", y = "Theoretical fraction exchanged [%]") } }
if (input[["export_theo_comparison_plot"]]){ cat("### Absolute values \n") p <- comparison_plot_theo_abs() + scale_color_manual(values = as.vector(comparison_plot_colors_chosen())) if(input[["theory"]] & input[["calc_type"]]=="absolute"){ p + coord_cartesian(ylim = c(input[["comp_plot_y_range"]][[1]], input[["comp_plot_y_range"]][[2]]), xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = input[["comparison_plot_title"]], x = input[["comparison_plot_x_label"]], y = input[["comparison_plot_y_label"]]) } else { p + coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]]))+ labs(title = paste0("Theoretical absolute value exchanged in state comparison in ", input[["chosen_time"]], " min"), x = "Position in sequence", y = "Theoretical absolute value exchanged [Da]") } }
if (input[["export_theo_comparison_plot_data"]]){ cat("## Theoretical Comparison Plot Data \n") cat("### Relative values \n") cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%.")) comparison_plot_data_theo() }
if (input[["export_theo_comparison_plot_data"]]){ cat("### Absolute values \n") comparison_plot_data_theo_abs() }
if (input[["export_woods_plot"]]){ cat("## Woods Plot \n") cat("### Relative values \n") if(has_modifications()){ cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.") } else{ if(input[["out_time"]] == 99999){ cat(paste0("Chosen control: ", input[["chosen_control"]], ".")) } else{ cat("No chosen control. \n") } } p <- differential_plot_exp() if(!input[["theory"]] & input[["calc_type"]] == "relative"){ p + coord_cartesian(ylim = c(input[["woods_plot_y_range"]][[1]], input[["woods_plot_y_range"]][[2]]), xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = input[["woods_plot_title"]], x = input[["woods_plot_x_label"]], y = input[["woods_plot_y_label"]]) } else { p + coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = paste0("Delta Fraction exchanged in ", input[["chosen_time"]], " min between ", gsub("_", " ", input[["state_first"]]), " and ", gsub("_", " ", input[["state_second"]])), x = "Position in sequence", y = "Delta Fraction exchanged between states [%]") } }
if (input[["export_woods_plot"]]){ cat("### Absolute values \n") p <- differential_plot_exp_abs() if(!input[["theory"]] & input[["calc_type"]] == "absolute"){ p + coord_cartesian(ylim = c(input[["woods_plot_y_range"]][[1]], input[["woods_plot_y_range"]][[2]]), xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = input[["woods_plot_title"]], x = input[["woods_plot_x_label"]], y = input[["woods_plot_y_label"]]) } else { p + coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = paste0("Delta Fraction exchanged in ", input[["chosen_time"]], " min between ", gsub("_", " ", input[["state_first"]]), " and ", gsub("_", " ", input[["state_second"]])), x = "Position in sequence", y = "Delta Absolute value exchanged between states [Da]") } }
if (input[["export_woods_plot_data"]]){ cat("## Woods Plot Data \n") cat("### Relative values \n") if(has_modifications()){ cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.") } else{ if(input[["out_time"]] == 99999){ cat(paste0("Chosen control: ", input[["chosen_control"]], ".")) } else{ cat("No chosen control. \n") } } differential_plot_data_exp() }
if (input[["export_woods_plot_data"]]){ cat("### Absolute values \n") differential_plot_data_exp_abs() }
if (input[["export_theo_woods_plot"]]){ cat("## Theoretical Woods Plot \n") cat("### Relative values \n") cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%.")) p <- differential_plot_theo() if(input[["theory"]] & input[["calc_type"]] == "relative"){ p + coord_cartesian(ylim = c(input[["woods_plot_y_range"]][[1]], input[["woods_plot_y_range"]][[2]]), xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = input[["woods_plot_title"]], x = input[["woods_plot_x_label"]], y = input[["woods_plot_y_label"]]) } else { p + coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = paste0("Delta Theoretical fraction exchanged in ", input[["chosen_time"]], " min between ", gsub("_", " ", input[["state_first"]]), " and ", gsub("_", " ", input[["state_second"]])), x = "Position in sequence", y = "Delta Theoretical fraction exchanged between states [%]") } }
if (input[["export_theo_woods_plot"]]){ cat("### Absolute values \n") p <- differential_plot_theo_abs() if(input[["theory"]] & input[["calc_type"]] == "absolute"){ p + coord_cartesian(ylim = c(input[["woods_plot_y_range"]][[1]], input[["woods_plot_y_range"]][[2]]), xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = input[["woods_plot_title"]], x = input[["woods_plot_x_label"]], y = input[["woods_plot_y_label"]]) } else { p + coord_cartesian(xlim = c(input[["plot_x_range"]][[1]], input[["plot_x_range"]][[2]])) + labs(title = paste0("Delta Theoretical fraction exchanged in ", input[["chosen_time"]], " min between ", gsub("_", " ", input[["state_first"]]), " and ", gsub("_", " ", input[["state_second"]])), x = "Position in sequence", y = "Delta Theoretical absoute value exchanged between states [Da]") } }
if (input[["export_theo_woods_plot_data"]]){ cat("## Theoretical Woods Plot Data \n") cat("### Relative values \n") cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%.")) differential_plot_data_theo() }
if (input[["export_theo_woods_plot_data"]]){ cat("### Absolute values \n") differential_plot_data_theo_abs() }
kin_valid <- length(input[["peptide_list_data_rows_selected"]]) > 0
if (input[["export_kin_plot"]]){ cat("## Uptake curve \n") if (kin_valid) { cat("### Relative values \n") if(has_modifications()){ cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.") } else{ if(input[["out_time"]] == 99999){ cat(paste0("Chosen control: ", input[["chosen_control"]], ".")) } else{ cat("No chosen control. \n") } } p <- kin_plot_exp() if(!input[["theory"]] & input[["calc_type"]]=="relative"){ p + coord_cartesian(ylim = c(input[["kin_plot_y_range"]][[1]], input[["kin_plot_y_range"]][[2]])) + labs(title = input[["kin_plot_title"]], x = input[["kin_plot_x_label"]], y = input[["kin_plot_y_label"]]) + theme(legend.position = "bottom", legend.title = element_blank()) } else { p + labs(title = "Uptake curve for chosen peptides", x = "Time points [min]", y = "Deuteration [%]") + scale_y_continuous(limits = c(0, 110)) + theme(legend.position = "bottom", legend.title = element_blank()) } } else { "Uptake curve cannot be shown - no peptides were selected" } }
if (input[["export_kin_plot"]]){ if (kin_valid) { cat("### Absolute values \n") p <- kin_plot_exp_abs() if (!input[["theory"]] & input[["calc_type"]]=="absolute"){ p + coord_cartesian(ylim = c(input[["kin_plot_y_range"]][[1]], input[["kin_plot_y_range"]][[2]])) + labs(title = input[["kin_plot_title"]], x = input[["kin_plot_x_label"]], y = input[["kin_plot_y_label"]]) + theme(legend.position = "bottom", legend.title = element_blank()) } else { p + labs(title = "Uptake curve for chosen peptides", x = "Time points [min]", y = "Deuteration [Da]") + scale_y_continuous(limits = c(0, NA)) + theme(legend.position = "bottom", legend.title = element_blank()) } } }
if (input[["export_kin_plot_data"]]){ cat("## Uptake curve Data \n") if (kin_valid){ cat("### Relative values \n") if(has_modifications()){ cat("Supplied file contains modified peptids. Maximal exchange control cannot be applied.") } else{ if(input[["out_time"]] == 99999){ cat(paste0("Chosen control: ", input[["chosen_control"]], ".")) } else{ cat("No chosen control. \n") } } kin_plot_exp_data() } else { "Uptake curve data cannot be shown - no peptides were selected" } }
if (input[["export_kin_plot_data"]]){ if (kin_valid) { cat("### Absolute values \n") kin_plot_exp_abs_data() } }
if (input[["export_theo_kin_plot"]]){ cat("## Theoretical Uptake curve Data \n") if (kin_valid){ cat("### Relative values \n") cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%.")) p <- kin_plot_theo() if(input[["theory"]] & input[["calc_type"]]=="relative"){ p + coord_cartesian(ylim = c(input[["kin_plot_y_range"]][[1]], input[["kin_plot_y_range"]][[2]])) + labs(title = input[["kin_plot_title"]], x = input[["kin_plot_x_label"]], y = input[["kin_plot_y_label"]]) + theme(legend.position = "bottom", legend.title = element_blank()) } else { p + labs(title = "Theoretical uptake curve for chosen peptides", x = "Time points [min]", y = "Deuteration [%]") + scale_y_continuous(limits = c(0, 110)) + theme(legend.position = "bottom", legend.title = element_blank()) } } else { "Theoretical uptake curve plot cannot be shown - no peptides were selected" } }
if (input[["export_theo_kin_plot"]]){ if (kin_valid) { cat("### Absolute values \n") p <- kin_plot_theo_abs() if(input[["theory"]] & input[["calc_type"]]=="absolute"){ p + coord_cartesian(ylim = c(input[["kin_plot_y_range"]][[1]], input[["kin_plot_y_range"]][[2]])) + labs(title = input[["kin_plot_title"]], x = input[["kin_plot_x_label"]], y = input[["kin_plot_y_label"]]) + theme(legend.position = "bottom", legend.title = element_blank()) } else { p + labs(title = "Theoretical uptake curve for chosen peptides", x = "Time points [min]", y = "Deuteration [Da]") + scale_y_continuous(limits = c(0, NA)) + theme(legend.position = "bottom", legend.title = element_blank()) } } }
if (input[["export_theo_kin_plot_data"]]){ cat("## Theoretical uptake curve Data \n") if (kin_valid){ cat("### Relative values \n") cat(paste0("Deuterium concentration: ", input[["deut_concentration"]], "%.")) kin_plot_theo_data() } else { "Theoretical uptake curve data cannot be shown - no peptides were selected" } }
if (input[["export_theo_kin_plot_data"]]){ if (kin_valid){ cat("### Absolute values \n") kin_plot_theo_abs_data() } }
if (input[["export_quality_control_plot"]]){ cat("## Quality Control Plot \n") cat("Quality control plot is based purely on experimental values.") qc_out() }
if (input[["export_quality_control_plot_data"]]){ cat("## Quality Control Plot Data \n") cat("Quality control plot data is based purely on experimental values.") quality_control_plot_data_out() }
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