ZScorePlot {RNAither} | R Documentation |
Plots the normalized intensity values for each well, together with a black line showing the mean, two green lines showing the standard deviation, and two red lines showing 2 standard deviations.
ZScorePlot(header, dataset, flag, col4plot, col4anno, plotTitle, showPlot)
header |
the header of a dataset file generated with generateDatasetFile |
dataset |
an R data frame generated with generateDatasetFile |
flag |
either 1 or 2. 1 if the dataset contains values per well, 2 if the dataset contains summarized values for each siRNA (e.g. a dataset summarized with summarizeReps ). |
col4plot |
a character string specifying the column whose values will be used for the plot |
col4anno |
a character string specifying the column that will be used for the plot annotation |
plotTitle |
the plot title |
showPlot |
0 or 1. 1 will open one or several plot windows in the R GUI, 0 will only save the plot(s) without opening windows. |
Plots the normalized intensity values for each well, together with a black line showing the mean, and two red lines showing 2 standard deviations. Clicking on the points shows the gene/siRNA name.
The plot is saved as a pdf and a png file named after the experiment name specified in the header concatenated with the plotTitle
.
The function returns the plot name.
data(exampleHeader, package="RNAither") data(exampleDataset, package="RNAither") normedvals <- ZScore(header, dataset, list("SigIntensity", 1)) ZScorePlot(normedvals[[1]], normedvals[[2]], 1, "SigIntensity", "GeneName", "Normed intensity values per well", 1)