sequencePlot: Sequence Plot

In idpr: Profiling and Analyzing Intrinsically Disordered Proteins in R

Description

This is a graphical function used to visualize numeric data along an amino acid sequence.

Usage

sequencePlot(
  position,
  property,
  hline = NA,
  propertyLimits = NA,
  dynamicColor = NA,
  customColors = NA,
  midpoint = hline,
  customTitle = NA
)

Arguments

position	numeric vector of residue positions. Typically c(1 : sequenceLength). ie a sequence with 215 amino acids has a vector of values 1 to 215. This is the X axis
property	vector of values, typically numeric. Equal in length to position. This is the Y axis.
hline, propertyLimits	optional, numeric values or numeric vectors. Prints horizontal lines. Set to NA to skip (default). *hline* specifies the location for a dashed, grey line to be printed underneath the plot's data line. Good for separating cutoff values. *propertyLimits* specifies the location for a solid, black line to be printed. Good for showing maximum and minimum values.
dynamicColor	optional vector. Typically numeric. Equal in length to position. Can be used to set colors based on values. Can be categorical (discrete) or continuous. Set to NA to skip (default).
customColors	optional vector of colors as character strings. Used to support custom plot colors. If property is a discrete scale, a character vector of colors with length = number of unique discrete observations is required. If property is a continuous scale, a character vector of the colors for c("highColor","lowColor","midColor"). Set NA to skip custom colors (default). Ignored if dynamicColor = NA.
midpoint	needed for proper scales of customColors. The default value is equal to hline (if provided). If there is no hline, the average of propertyLimits is the midpoint (if provided). If neither is provided, the value will be NA. The user can explicitly assign the midpoint to avoid this or to overwrite the defaults.
customTitle	optional, character string. Allows adding custom title. Set to NA to skip (default).

Value

a ggplot

Examples

#Get a data frame returned from another function
aaVector <- c("A", "C", "D", "E", "F",
           "G", "H", "I", "K", "L",
           "M", "N", "P", "Q", "R",
           "S", "T", "V", "W", "Y")
exampleDF <- chargeCalculationGlobal(sequence = aaVector)
head(exampleDF)
#Making a sequence plot
sequencePlot(
  position = exampleDF$Position,
  property = exampleDF$Charge)

#Change the horizontal lines
sequencePlot(
position = exampleDF$Position,
property = exampleDF$Charge,
hline = 0.0,
propertyLimits = c(-1.0, 1.0))

#Adding a dynamic colors based on the property values
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")

idpr documentation built on Dec. 26, 2020, 6 p.m.