Description Usage Arguments Value Author(s) Examples
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.
1 2 3 4 5 6 7 8 9 | 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)
|
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 |
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.
Menghao Yu
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | 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)
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