## ---- echo = FALSE, message = FALSE, warning = FALSE, results='asis'---------- library(HaDeX) library(ggplot2) library(knitr) library(DT) library(dplyr) opts_chunk$set(fig.width = 7, fig.height = 5) knitr::opts_chunk$set(dev = "png", dev.args = list(type = "cairo-png")) ## ----echo=FALSE,results='asis'------------------------------------------------ read.csv2("comparison.csv") %>% datatable(options = list(dom = "t", ordering = FALSE, paging = FALSE), rownames = FALSE, style = "bootstrap") %>% formatStyle(c("MSTools", "MEMHDX", "Deuteros", "HaDeX"), backgroundColor = styleEqual(c("Yes", "No"), c("#00BFFF", "#FF8C91"))) ## ----warning=FALSE, message=FALSE, echo = FALSE------------------------------- datatable( data = data.frame("Column Name" = c("Protein", "Start", "End", "Sequence", "Modification", "Fragment", "MaxUptake", "MHP", "State", "Exposure", "File", "z", "RT", "Inten", "Center"), "Column Type" = c("Character", "Integer", "Integer", "Character", "Logic", "Logic", "Numeric", "Numeric", "Character", "Numeric", "Character", "Integer", "Numeric", "Numeric", "Numeric")), rownames = FALSE, style = "bootstrap", list(dom = "t", ordering = FALSE, paging = FALSE, autoWidth = TRUE)) ## ----warning=FALSE------------------------------------------------------------ dat <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_190304_Nucb2_EDTA_CaCl2_test02_clusterdata.csv")) ## ----warning=FALSE, message=FALSE, echo=FALSE--------------------------------- dat_temp <- read.csv(system.file(package = "HaDeX", "HaDeX/data/KD_190304_Nucb2_EDTA_CaCl2_test02_clusterdata.csv")) dat_temp %>% filter(File == "KD_190119_gg_Nucb2_CaCl2_10s_01", Sequence == "KQFEHLNHQNPDTFEPKDLDML", Exposure == 0.167) %>% select(Sequence, File, z, RT, Inten, Center) ## ----warning=FALSE------------------------------------------------------------ calc_dat <- prepare_dataset(dat, in_state_first = "gg_Nucb2_EDTA_0.001", chosen_state_first = "gg_Nucb2_EDTA_25", out_state_first = "gg_Nucb2_EDTA_1440", in_state_second = "gg_Nucb2_CaCl2_0.001", chosen_state_second = "gg_Nucb2_CaCl2_25", out_state_second = "gg_Nucb2_CaCl2_1440") ## ----warning=FALSE------------------------------------------------------------ comparison_plot(calc_dat = calc_dat, theoretical = TRUE, relative = TRUE, state_first = "Nucb2 Factor 1", state_second = "Nucb2 Factor 2") + labs(title = "Theoretical fraction exchanged in state comparison in 25 min time") ## ----warning=FALSE------------------------------------------------------------ comparison_plot(calc_dat = calc_dat, theoretical = TRUE, relative = FALSE, state_first = "Nucb2 Factor 1", state_second = "Nucb2 Factor 2") + labs(title = "Theoretical fraction exchanged in state comparison in 25 min time") ## ----warning=FALSE------------------------------------------------------------ comparison_plot(calc_dat = calc_dat, theoretical = FALSE, relative = TRUE, state_first = "Nucb2 Factor 1", state_second = "Nucb2 Factor 2") + labs(title = "Fraction exchanged in state comparison in 25 min time") ## ----warning=FALSE------------------------------------------------------------ comparison_plot(calc_dat = calc_dat, theoretical = FALSE, relative = FALSE, state_first = "Nucb2 Factor 1", state_second = "Nucb2 Factor 2") + labs(title = "Fraction exchanged in state comparison in 25 min time") ## ----warning=FALSE------------------------------------------------------------ woods_plot(calc_dat = calc_dat, theoretical = TRUE, relative = TRUE) + labs(title = "Theoretical fraction exchanged between states in 25 min time") ## ----warning=FALSE------------------------------------------------------------ woods_plot(calc_dat = calc_dat, theoretical = TRUE, relative = FALSE) + labs(title = "Theoretical fraction exchanged between states in 25 min time") ## ----warning=FALSE------------------------------------------------------------ woods_plot(calc_dat = calc_dat, theoretical = FALSE, relative = TRUE) + labs(title = "Theoretical fraction exchanged between states in 25 min time") ## ----warning=FALSE------------------------------------------------------------ woods_plot(calc_dat = calc_dat, theoretical = FALSE, relative = FALSE) + labs(title = "Theoretical fraction exchanged between states in 25 min time") ## ----------------------------------------------------------------------------- calculate_confidence_limit_values(calc_dat = calc_dat, confidence_limit = 0.99, theoretical = FALSE, relative = TRUE) ## ----------------------------------------------------------------------------- add_stat_dependency(calc_dat, confidence_limit = 0.98, theoretical = FALSE, relative = TRUE) ## ----warning = FALSE---------------------------------------------------------- (kin_YYDEYL_gg_Nucb2_CaCl2 <- calculate_kinetics(dat = dat, protein = "db_Nucb2", sequence = "YYDEYL", state = "gg_Nucb2_CaCl2", start = 45, end = 50, time_in = 0.001, time_out = 1440)) ## ----warning = FALSE---------------------------------------------------------- (kin_YYDEYL_gg_Nucb2_EDTA <- calculate_kinetics(dat = dat, protein = "db_Nucb2", sequence = "YYDEYL", state = "gg_Nucb2_EDTA", start = 45, end = 50, time_in = 0.001, time_out = 1440)) ## ----warning = FALSE---------------------------------------------------------- bind_rows(kin_YYDEYL_gg_Nucb2_CaCl2, kin_YYDEYL_gg_Nucb2_EDTA) %>% plot_kinetics(theoretical = TRUE, relative = TRUE) ## ----warning = FALSE---------------------------------------------------------- bind_rows(kin_YYDEYL_gg_Nucb2_CaCl2, kin_YYDEYL_gg_Nucb2_EDTA) %>% plot_kinetics(theoretical = TRUE, relative = FALSE) ## ----warning = FALSE---------------------------------------------------------- bind_rows(kin_YYDEYL_gg_Nucb2_CaCl2, kin_YYDEYL_gg_Nucb2_EDTA) %>% plot_kinetics(theoretical = FALSE, relative = TRUE) ## ----warning = FALSE---------------------------------------------------------- bind_rows(kin_YYDEYL_gg_Nucb2_CaCl2, kin_YYDEYL_gg_Nucb2_EDTA) %>% plot_kinetics(theoretical = FALSE, relative = FALSE) ## ----warning=FALSE------------------------------------------------------------ reconstruct_sequence(dat) ## ----warning=FALSE------------------------------------------------------------ plot_coverage(dat, chosen_state = "gg_Nucb2_CaCl2") plot_position_frequency(dat, chosen_state = "gg_Nucb2_CaCl2") ## ----warning=FALSE------------------------------------------------------------ result <- quality_control(dat = dat, state_first = "gg_Nucb2_EDTA", state_second = "gg_Nucb2_CaCl2", chosen_time = 1, in_time = 0.001) ## ----warning=FALSE------------------------------------------------------------ ggplot(result) + geom_line(aes(x = out_time, y = avg_err_state_first, color = "Average error (first state)")) + geom_line(aes(x = out_time, y = avg_err_state_second, color = "Average error (second state)")) + scale_x_log10() + labs(x = "log(time) [min]", y = "Average uncertainty", title = "Uncertainty change") + theme_bw(base_size = 11) + theme(legend.position = "bottom", legend.title = element_blank()) ## ----warning=FALSE,echo=FALSE------------------------------------------------- example_qc <- rbind(data.frame(x = c(10, 25, 60, 1440), y = c(0.008, 0.0075, 0.007, 0.0065), type = "Uncertainty decreases too slowly\nExperiment should be prolonged", Assessment = "Alter experimental settings"), data.frame(x = c(10, 25, 60, 1440), y = c(0.008, 0.001, 0.001, 0.001), type = "Uncertainty decreases too quickly\nExperiment should have more early timepoints", Assessment = "Alter experimental settings"), data.frame(x = c(10, 25, 60, 1440), y = c(0.008, 0.004, 0.003, 0.001), type = "Uncertainty decreases properly", Assessment = "Experiment conducted properly")) ggplot(example_qc, aes(x = x, y = y, color = Assessment)) + geom_line() + geom_point() + facet_wrap(~ type, ncol = 1) + theme_bw() + theme(legend.position = "bottom") ## ----warning=FALSE------------------------------------------------------------ library(HaDeX) # file import dat_1 <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_180110_CD160_HVEM.csv")) ## ----warning=FALSE------------------------------------------------------------ reconstruct_sequence(dat_1) plot_position_frequency(dat_1, chosen_state = "CD160") ## ----warning=FALSE------------------------------------------------------------ # calculate data calc_dat_1 <- prepare_dataset(dat = dat_1, in_state_first = "CD160_0.001", chosen_state_first = "CD160_1", out_state_first = "CD160_1440", in_state_second = "CD160_HVEM_0.001", chosen_state_second = "CD160_HVEM_1", out_state_second = "CD160_HVEM_1440") # theoretical comparison plot - relative values comparison_plot(calc_dat = calc_dat_1, theoretical = TRUE, relative = TRUE, state_first = "CD160", state_second = "CD160_HVEM") ## ----warning=FALSE------------------------------------------------------------ # experimental comparison plot - relative values comparison_plot(calc_dat = calc_dat_1, theoretical = FALSE, relative = TRUE, state_first = "CD160", state_second = "CD160_HVEM") ## ----warning=FALSE------------------------------------------------------------ # theoretical comparison plot - absolute values comparison_plot(calc_dat = calc_dat_1, theoretical = TRUE, relative = FALSE, state_first = "CD160", state_second = "CD160_HVEM") # experimental comparison plot - absolute values comparison_plot(calc_dat = calc_dat_1, theoretical = FALSE, relative = FALSE, state_first = "CD160", state_second = "CD160_HVEM") ## ----warning=FALSE------------------------------------------------------------ # theoretical Woods plot - relative values woods_plot(calc_dat = calc_dat_1, theoretical = TRUE, relative = TRUE) + coord_cartesian(ylim = c(-.2, .2)) ## ----warning=FALSE------------------------------------------------------------ # experimental Woods plot - relative values woods_plot(calc_dat = calc_dat_1, theoretical = FALSE, relative = TRUE) + coord_cartesian(ylim = c(-.2, .2)) ## ----warning=FALSE------------------------------------------------------------ # theoretical Woods plot - absolute values woods_plot(calc_dat = calc_dat_1, theoretical = TRUE, relative = FALSE) + labs(title = "Theoretical fraction exchanged between states in 1 min time") # experimental Woods plot - absolute values woods_plot(calc_dat = calc_dat_1, theoretical = FALSE, relative = FALSE) + labs(title = "Fraction exchanged between states in 1 min time") # quality control - relative values (result <- quality_control(dat = dat_1, state_first = "CD160", state_second = "CD160_HVEM", chosen_time = 1, in_time = 0.001)) # example quality control visualisation library(ggplot2) ggplot(result) + geom_line(aes(x = out_time, y = avg_err_state_first, color = "Average error (first state)")) + geom_line(aes(x = out_time, y = avg_err_state_second, color = "Average error (second state)")) + scale_x_log10() + ylim(0, 0.05) + labs(x = "log(time) [min]", y = "Average uncertainty", title = "Uncertainty change in out time") + theme(legend.title = element_blank(), legend.position = "bottom") ## ----warning=FALSE------------------------------------------------------------ library(HaDeX) # file import dat_2 <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_190304_Nucb2_EDTA_CaCl2_test02_clusterdata.csv")) # protein sequence reconstruction reconstruct_sequence(dat_2) # calculate data calc_dat_2 <- prepare_dataset(dat = dat_2, in_state_first = "gg_Nucb2_EDTA_0.001", chosen_state_first = "gg_Nucb2_EDTA_25", out_state_first = "gg_Nucb2_EDTA_1440", in_state_second = "gg_Nucb2_CaCl2_0.001", chosen_state_second = "gg_Nucb2_CaCl2_25", out_state_second = "gg_Nucb2_CaCl2_1440") # theoretical comparison plot - relative values comparison_plot(calc_dat = calc_dat_2, theoretical = TRUE, relative = TRUE, state_first = "Nucb2 Factor 1", state_second = "Nucb2 Factor 2") + labs(title = "Theoretical fraction exchanged in \nstate comparison in 25 min time") # experimental comparison plot - relative values comparison_plot(calc_dat = calc_dat_2, theoretical = FALSE, relative = TRUE, state_first = "Nucb2 Factor 1", state_second = "Nucb2 Factor 2") + labs(title = "Fraction exchanged in \nstate comparison in 25 min time") # theoretical comparison plot - absolute values comparison_plot(calc_dat = calc_dat_2, theoretical = TRUE, relative = FALSE, state_first = "Nucb2 Factor 1", state_second = "Nucb2 Factor 2") + labs(title = "Theoretical fraction exchanged in \nstate comparison in 25 min time") # experimental comparison plot - absolute values comparison_plot(calc_dat = calc_dat_2, theoretical = FALSE, relative = FALSE, state_first = "Nucb2 Factor 1", state_second = "Nucb2 Factor 2") + labs(title = "Fraction exchanged in \nstate comparison in 25 min time") # theoretical Woods plot - relative values woods_plot(calc_dat = calc_dat_2, theoretical = TRUE, relative = TRUE) + labs(title = "Theoretical fraction exchanged between states in 25 min time") + coord_cartesian(ylim = c(-.5, .7)) # experimental Woods plot - relative values woods_plot(calc_dat = calc_dat_2, theoretical = FALSE, relative = TRUE) + labs(title = "Fraction exchanged between states in 25 min time") + coord_cartesian(ylim = c(-.5, .7)) # theoretical Woods plot - absolute values woods_plot(calc_dat = calc_dat_2, theoretical = TRUE, relative = FALSE) + labs(title = "Theoretical fraction exchanged between states in 25 min time") # experimental Woods plot - absolute values woods_plot(calc_dat = calc_dat_2, theoretical = FALSE, relative = FALSE) + labs(title = "Fraction exchanged between states in 25 min time") # quality control (result <- quality_control(dat = dat_2, state_first = "gg_Nucb2_EDTA", state_second = "gg_Nucb2_CaCl2", chosen_time = 25, in_time = 0.001)) # example quality control visualisation - relative values library(ggplot2) ggplot(result[result["out_time"]>=1,]) + geom_line(aes(x = out_time, y = avg_err_state_first, color = "Average error (first state)")) + geom_line(aes(x = out_time, y = avg_err_state_second, color = "Average error (second state)")) + scale_x_log10() + labs(x = "log(time) [min]", y = "Average uncertainty", title = "Uncertainty change") + theme(legend.position = "bottom", legend.title = element_blank())