ssa_plot: ggstride

In ugerlevik/ggstride: An R Package for Protein 2D Structure Analysis and Visualization

ggstride

Description

ssa_plot() returns a plot that contains percentage of secondary structures observed along the trajectories per residue by comparing the two ssa data frames obtained by ssa().

Usage

ssa_plot(
  ssa1,
  ssa2,
  name1 = "Wild-type",
  name2,
  resid1 = as.numeric(gsub("\\D+", "", colnames(ssa1)[1])),
  resid2 = as.numeric(gsub("\\D+", "", colnames(ssa1)[length(colnames(ssa1))])),
  color_number1 = 1,
  color_number2 = 2
)

Arguments

ssa1:	the ssa data frame calculated for trajectory 1, calculated by ggstride::ssa()
ssa2:	the ssa data frame calculated for trajectory 2, calculated by ggstride::ssa()
name1:	assign a name for your trajectory 1
name2:	assign a name for your trajectory 2
resid1:	residue id of the first residue of the region you want to visualize
resid2:	residue id of the last residue of the region you want to visualize
color_number1:	(between 1 and 7) select a color from jama palette of ggsci for the ssa of trajectory 1
color_number2:	(between 1 and 7) select a color from jama palette of ggsci for the ssa of trajectory 2

Value

plot

Examples

ssa_plot(ssa1 = ssa_WT, ssa2 = ssa_mutant,
name1 = "Wild-type", name2 = "Leu656Phe",
resid1 = 500, resid2 = 525,
color_number1 = 1, color_number2 = 2)

ggstride::ssa_plot(ssa1, ssa2, name1 = "Wild-type", color_number1 = 1, name2, color_number2)

ugerlevik/ggstride documentation built on Feb. 7, 2023, 11:13 a.m.