pymol_script_significant_residue {HDXBoxeR} | 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 being colored by maximum uptake from significant peptides per residues.
pymol_script_significant_residue(
df,
path = "",
ranges = c(-Inf, seq(-30, 30, by = 10), Inf),
pv_cutoff = 0.01,
replicates = 3
)
df |
average data frame. Generated using ave_timepoint() 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 colors assigned per residues by maximum uptake per residue
file_nm<-system.file("extdata", "All_results_table.csv", package = "HDXBoxeR")
a<- output_tp(file_nm)
pymol_script_significant_residue(df=a, path=tempdir(), replicates=3, pv_cutoff=0.01,
ranges=c(-Inf,-40, -30,-20,-10, 0,10, 20,30,40, Inf) )
pymol_script_significant_residue(df=a, path=tempdir())