Nothing
## ----include = FALSE----------------------------------------------------------
library(ragg)
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 6,
fig.height = 5,
dev = "ragg_png"
)
## ----message = FALSE----------------------------------------------------------
library(spant)
## ----message = FALSE----------------------------------------------------------
get_mol_names()
## ----message = FALSE----------------------------------------------------------
ins <- get_mol_paras("ins")
print(ins)
## ----message = FALSE----------------------------------------------------------
sim_mol(ins, ft = 300e6, N = 4096) |> lb(2) |> plot(xlim = c(3.8, 3.1))
## ----message = FALSE----------------------------------------------------------
ins_sim <- sim_mol(ins, seq_spin_echo_ideal, ft = 300e6, N = 4086, TE = 0.03)
ins_sim |> lb(2) |> plot(xlim = c(3.8, 3.1))
## ----message = FALSE, fig.height = 8------------------------------------------
sim_fn <- function(TE) {
te_sim <- sim_mol(ins, seq_spin_echo_ideal, ft = 300e6, N = 4086, TE = TE)
lb(te_sim, 2)
}
te_vals <- seq(0, 2, 0.4)
lapply(te_vals, sim_fn) |> stackplot(y_offset = 150, xlim = c(3.8, 3.1),
labels = paste(te_vals * 100, "ms"))
## ----message = FALSE----------------------------------------------------------
get_uncoupled_mol("Lip13", c(1.3, 1.4), c("1H", "1H"), c(2, 1), c(10, 10),
c(1, 1)) |> sim_mol() |> plot(xlim = c(2, 0.8))
## ----message = FALSE----------------------------------------------------------
nucleus_a <- rep("1H", 4)
chem_shift_a <- c(4.0974, 1.3142, 1.3142, 1.3142)
j_coupling_mat_a <- matrix(0, 4, 4)
j_coupling_mat_a[2,1] <- 6.933
j_coupling_mat_a[3,1] <- 6.933
j_coupling_mat_a[4,1] <- 6.933
spin_group_a <- list(nucleus = nucleus_a, chem_shift = chem_shift_a,
j_coupling_mat = j_coupling_mat_a, scale_factor = 1,
lw = 2, lg = 0)
nucleus_b <- c("1H")
chem_shift_b <- c(2.5)
j_coupling_mat_b <- matrix(0, 1, 1)
spin_group_b <- list(nucleus = nucleus_b, chem_shift = chem_shift_b,
j_coupling_mat = j_coupling_mat_b, scale_factor = 3,
lw = 2, lg = 0)
source <- "This text should include a reference on the origin of the chemical shift and j-coupling values."
custom_mol <- list(spin_groups = list(spin_group_a, spin_group_b), name = "Cus",
source = source, full_name = "Custom molecule")
class(custom_mol) <- "mol_parameters"
## ----message = FALSE----------------------------------------------------------
print(custom_mol)
custom_mol |> sim_mol() |> lb(2) |> zf() |> plot(xlim = c(4.4, 0.5))
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