fs.line.plot: Line plot of Functionality Score vs. some other axis

In seshadrilab/flowHelpers: Collection of helper functions for analyzing FCM data

Description

This function creates a line plot of Functionality Score vs. some other axis, like those generated by the GenericCOMPASSWrapper.R script. Some formatting of the input data table is required, so it is not very "generic".

Usage

fs.line.plot(fsData, outdir = NULL, xaxis, yaxis, groupName,
  addBox = FALSE, ylimits = NULL, fileSuffix = NULL,
  condition = NULL)

Arguments

fsData	data table to plot
outdir	(Optional) will save plot to a file in this directory, if provided
xaxis	column in fsData for stratifying x-axis
yaxis	column in fsData for the y-axis (probably functionality score)
groupName	column name which identifies groups (e.g. individuals, for connecting line plots)
addBox	(Optional) A boolean. Adds boxplots for each x-axis value if set to True.
ylimits	(Optional) numeric vector specifying upper and lower y-axis limits
fileSuffix	(Optional) What to add to end of filename

Value

Line plot of FS scores, unless outdir is specified

Examples

## Not run: 
# Create the fsData table from the COMPASS output FS text file.
fsFile <- "/home/path/to/CD8/8+_CMV/FS_8+_CMV.txt"
ylims <- c(0, 0.15)
fsTable <- read.table(fsFile, header=TRUE, sep="\t", check.names=FALSE)
cellSubset <- as.character(fsTable[,"CellSubset"])
condition <- as.character(fsTable[,conditioncol])
fsData1 <- t(fsTable[,3:length(colnames(fsTable))])
fsData1 <- cbind(fsData1, ldply(rownames(fsData1), .fun = function(x) {strsplit(x, ", Time ")[[1]]}))
colnames(fsData1) <- c("FunctionalityScore", "PTID", "Time")
# Draw the line plot
fs.line.plot(fsData=fsData1, xaxis="Time", yaxis="FunctionalityScore", groupName="PTID", addBox=TRUE, ylimits=ylims)

## End(Not run)

seshadrilab/flowHelpers documentation built on May 23, 2019, 4:05 a.m.