## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width = 6, fig.height = 4 ) ## ----------------------------------------------------------------------------- #BiocManager::install("idpr") ## ----------------------------------------------------------------------------- #devtools::install_github("wmm27/idpr") ## ----setup-------------------------------------------------------------------- library(idpr) #load the idpr package ## ----------------------------------------------------------------------------- P53_HUMAN <- TP53Sequences[2] print(P53_HUMAN) ## ----------------------------------------------------------------------------- tendencyDF <- structuralTendency(sequence = P53_HUMAN) head(tendencyDF) chargeDF <- chargeCalculationGlobal(sequence = P53_HUMAN, includeTermini = FALSE) head(chargeDF) ## ----------------------------------------------------------------------------- sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency) sequenceMap( sequence = as.character(chargeDF$AA), property = chargeDF$Charge, #character vector customColors = c("blue", "red", "grey30")) ## ----------------------------------------------------------------------------- sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "AA") #Only AA residue Labels sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "number") #Only residue numner labels ## ----------------------------------------------------------------------------- sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "number", labelLocation = "on") #Residue numbers printed on the sequence graphic sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "number", labelLocation = "below") #Residue numbers printed below the sequence graphic ## ----------------------------------------------------------------------------- sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "number", labelLocation = "on", rotationAngle = 90) ## ----------------------------------------------------------------------------- sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "number", labelLocation = "on", everyN = 1) #Every residue sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "number", labelLocation = "on", everyN = 2) #Every 2nd (or every other) sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "number", labelLocation = "on", everyN = 10) #Every 10th residue is printed ## ----------------------------------------------------------------------------- sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "number", labelLocation = "on", nbResidues = 15) #15 residues each row sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, labelType = "number", labelLocation = "on", nbResidues = 45, rotationAngle = 90) #45 residues each row ## ----------------------------------------------------------------------------- sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, customColors = c("#999999", "#E69F00", "#56B4E9")) ## ----------------------------------------------------------------------------- sequenceMap( sequence = as.character(chargeDF$AA), property = chargeDF$Charge, customColors = c("purple", "pink", "grey90") ) ## ----------------------------------------------------------------------------- library(ggplot2) ggSequence <- sequenceMap( sequence = tendencyDF$AA, property = tendencyDF$Tendency, nbResidues = 40, customColors = c("#999999", "#E69F00", "#56B4E9")) # Adding Annotations of DNA Binding from UniProt ggSequence <- ggSequence + annotate("segment", x = 21, xend = 40.5, y = 8.05, yend = 8.05, color = "#FF3562", size = 1.5) + annotate("segment", x = 1, xend = 12.5, y = 3.05, yend = 3.05, color = "#FF3562", size = 1.5) + annotate("segment", x = 1, xend = 40.5, y = c(7:4) + 0.05, yend = c(7:4) + 0.05, color = "#FF3562", size = 1.5) + annotate("segment", x = 34, xend = 36, y = 0.65, yend = 0.65, color = "#FF3562", size = 1.5) + annotate("text", x = 36.35, y = 0.65, label = "= DNA Binding", size = 3.5, hjust = 0) # Adding a plot title ggSequence <- ggSequence + labs(title = "P53 Structural Tendency") + theme(plot.title = element_text(hjust = 0.5, vjust = 2.5)) # Adding point and text annotations ggSequence <- ggSequence + geom_point(aes(x = 2.5, #column 2 y = 4), #row 4 shape = 8, show.legend = FALSE, inherit.aes = FALSE) + annotate("text", x = 4.5, y = 4.3, label = "Metal Binding", size = 3) plot(ggSequence) ## ----------------------------------------------------------------------------- coord_DF <- sequenceMapCoordinates(P53_HUMAN, nbResidues = 40) head(coord_DF) ## ----------------------------------------------------------------------------- exampleDF <- chargeCalculationGlobal(P53_HUMAN, includeTermini = FALSE) #Making a sequence plot sequencePlot( position = exampleDF$Position, property = exampleDF$Charge) #Adding a dynamic colors based on the property values and horizontal lines sequencePlot( position = exampleDF$Position, property = exampleDF$Charge, hline = 0.0, propertyLimits = c(-1.0, 1.0), dynamicColor = exampleDF$Charge, customColors = c("red", "blue", "grey50"), customTitle = "Charge of Each Residue / Terminus") ## ----------------------------------------------------------------------------- citation("ggplot2") ## ----------------------------------------------------------------------------- R.version.string ## ----------------------------------------------------------------------------- as.data.frame(Sys.info()) ## ----results="asis"----------------------------------------------------------- citation()