ImportData: NORMAL BACTERIAL GRAPHICAL USAGE

In Menghao-diandian/NormalBacterialGraphicalUsage: Normal Bacterial Graphical Usage

Description

ImportData function imports and checks experiment data. CalMean calculates mean of imported data. CalSD calculates standard deviation of imported data. BarPlot creates bar plot for normal phenotypic assays in several testing groups. GrowthCurve creates line chart to show bacterial growth condition.

Usage

ImportData(myfile, rep, measurementPos, strainName, conditionName)
CalMean(myData, measurementPos, StrainColName = "Strain", conditionColName,
strainName,conditionName)
CalSD(myData, measurementPos, StrainColName = "Strain", conditionColName, 
strainName, conditionName)
BarPlot(myData, measurementPos, StrainColName = "Strain", conditionColName,
strainName, conditionName, ylabName)
GrowthCurve(myData, measurementPos, StrainColName = "Strain", 
conditionColName, strainName, timePoint)

Arguments

myfile	myfile is the name of a csv file, refer to data(Test1) for proper format, missing data is not allowed
rep	Replication number of each experiment setting, should be same among all settings
measurementPos	Number of the column which stores measurement data
strainName	Name of tested strains selected to be plotted. In GrowthCurve funciton, the length of strainName should be larger than 1.
conditionName	Tested conditions selected to be plotted. In GrowthCurve funciton, the length of conditionName should be larger than 1.
myData	Imported experiment data, refer to data(Test1) for proper format
StrainColName	In imported data, the name of the column which stores strain name
conditionColName	In imported data, the name of the column which stores testing condition
ylabName	Name of y-axis in exported bar plot
timePoint	Time point at which OD600 is measured

Value

ImportData returns the content of the imported data. CalMean returns mean of each tested group in a matrix. CalSD returns standard deviation of each tested group in a matrix. BarPlot a bar plot indicating the difference of several bacterial strains in several conditions. GrowthCurve a line chart indicating the growth condition of several bacterial strains.

Author(s)

Menghao Yu

Examples

mypath <- system.file ("extdata", "Test1.csv", 
                       package = "NormalBacterialGraphicalUsage")

a <- c("WT", "clpXP", "clpXP(pXP)") 
b <- c(24, 48)
ImportData (mypath, rep = 3, measurementPos = 3, 
            strainName = a, conditionName = b)

data(Test1)
CalMean (Test1, measurementPos = 3, 
         StrainColName = "Strain", 
         conditionColName = "Time", 
         strainName = a,
         conditionName = b)
         
CalSD (Test1, measurementPos = 3, 
       StrainColName = "Strain", 
       conditionColName = "Time",
       strainName = a,
       conditionName = b)

BarPlot (Test1, measurementPos = 3, 
         StrainColName = "Strain", 
         conditionColName = "Time", 
         strainName = a, conditionName = b, 
         ylabName = "Distance (mm)")
         
data(Test2)
d <- c("WT(p)", "#3(p)", "#3(pT)")
e <- c(3, 6, 9, 12, 15, 18, 21, 24)
GrowthCurve (Test2, measurementPos = 3, 
             StrainColName = "Strain", 
             conditionColName = "Time",
             strainName = d, timePoint = e)

Menghao-diandian/NormalBacterialGraphicalUsage documentation built on May 13, 2019, 10:59 p.m.