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inst/doc/HaDeX.R
In HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data
## ---- 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())
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## ---- 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())
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