View source: R/pymol_script_significant_residue_proc.R
pymol_script_significant_residue_proc | R Documentation |
Function write a script that can be used in pymol to color structure. Number of colors and corresponding to them ranges can be defined by user. Residues are colored by average procent_deuteration from the significant peptides per residues.
pymol_script_significant_residue_proc(
input_up,
input_proc,
path = "",
ranges = c(-Inf, seq(-30, 30, by = 10), Inf),
pv_cutoff = 0.01,
replicates = 3
)
input_up |
Dataframe with organized deuteration uptake. Input generated using output_tp() function. |
input_proc |
Dataframe with organized procent deuteration data. Input generated using output_tp_proc() function. |
path |
location where the Pymol scripts will be saved |
ranges |
ranges for coloring scheme. Default set to c(-Inf, seq(-30, 30, by=10), Inf) |
pv_cutoff |
p-value cutoff here set up to 0.01 |
replicates |
number of replicates in sample. Default set to 3. |
pymol script with residues colored based on average of procent deuteration per residue.
file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
a_up<- output_tp(file_nm)
a_proc<- output_tp(file_nm, percent=TRUE)
pymol_script_significant_residue_proc(input_proc=a_proc,
input_up=a_up, path=tempdir(), replicates=3, pv_cutoff=0.01,
ranges=c(-Inf,-40, -30,-20,-10, 0,10, 20,30,40, Inf))
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