inst/doc/Fiscore_vignette.R

In Fiscore: Effective Protein Structural Data Visualisation and Exploration

## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE,fig.width=8, fig.height=6)


## ----message=FALSE, warning=FALSE---------------------------------------------
library(Fiscore)

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pdb_path<- system.file("extdata", "6kz5.pdb", package="Fiscore")


pdb_df<-PDB_process(pdb_path)
pdb_df


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pdb_path<-system.file("extdata", "6kz5_A.pdb", package="Fiscore")
pdb_df<-PDB_prepare(pdb_path)
head(pdb_df)


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phi_psi_plot(pdb_df)


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phi_psi_bar_plot(pdb_df)


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phi_psi_interactive(pdb_df)


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B_plot_normalised(pdb_df)


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phi_psi_3D(pdb_df)


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Fi_score_plot(pdb_df)

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Fi_score_region(pdb_df,50,70)

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Fiscore_secondary(pdb_df)

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hydrophobicity_plot(pdb_df,window = 9,weight = 25,model = "linear")

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hydrophobicity_plot(pdb_df,window = 9,weight = 25,model = "exponential")

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df<-cluster_ID(pdb_df)



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df<-cluster_ID(pdb_df,clusters = 5, modelNames = "VVI")


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density_plots(pdb_df)

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density_plots(pdb_df, df)