displayHTS (version 1.0)

imageDesign.fn: Plate Design Image

Description

A function that displays the image of well designs in a plate.

Usage

imageDesign.fn(dataOnePlate.df, wellName = NA, rowName, colName, wells = NULL, colors = NULL, title = " ")

Arguments

dataOnePlate.df

The data for one plate including at least three columns for well names, rows and columns, respectively.

wellName

Name of the column in dataOnePlate.df indicating well types.

rowName

Name of the column in dataOnePlate.df indicating row numbers in a plate.

colName

Name of the column in dataOnePlate.df indicating column numbers in a plate.

wells

Names for unique wells.

colors

Colors for corresponding unique wells.

title

Title of the image.

References

Zhang XHD, Zhang ZZ. 2013. displayHTS: a R package displaying data and results from high-throughput screening experiments. Bioinformatics (submitted). Zhang XHD, 2011. Optimal High-Throughput Screening: Practical Experimental Design and Data Analysis for Genome-scale RNAi Research. Cambridge University Press, Cambridge, UK Zhang XHD, 2008. Novel analytic criteria and effective plate designs for quality control in genome-wide RNAi screens. Journal of Biomolecular Screening 13(5): 363-377 Zhang XHD, Espeseth AS, Johnson E, Chin J, Gates A, Mitnaul L, Marine SD, Tian J, Stec EM, Kunapuli P, Holder DJ, Heyse JF, Stulovici B, Ferrer M. 2008. Integrating experimental and analytic approaches to improve data quality in genome-wide RNAi screens. Journal of Biomolecular Screening 13(5): 378-389

See Also

imageIntensity.fn, dualFlashlight.fn, plateWellSeries.fn

Examples

# for control image
 data(HTSdataSort)
 wells = as.character(unique(HTSdataSort[, "WELL_USAGE"])); wells
 colors = c("black",  "yellow", "grey", "blue", "skyblue", "green", "red")
 plate.vec = as.vector(HTSdataSort[,"BARCODE"]); plates=unique(plate.vec)
 data.df = HTSdataSort[plate.vec==plates[1], c("XPOS","YPOS","WELL_USAGE")]
 imageDesign.fn(dataOnePlate.df=data.df, wellName="WELL_USAGE", rowName="XPOS",
                 colName="YPOS", wells=wells, colors=colors)

# for hit and control image
 data(HTSresults)
 condtSample = HTSresults[, "WELL_USAGE"] == "Sample"
 condtUp = HTSresults[,"ssmd"] >= 1 & HTSresults[,"mean"] >= log2(1.2)
 condtDown = HTSresults[,"ssmd"] <= -1 & HTSresults[,"mean"] <= -log2(1.2)
 sum(condtSample & (condtUp | condtDown) )/sum(condtSample)
 hit.vec = as.character(HTSresults[, "WELL_USAGE"])
 hit.vec[ condtSample & condtUp ] = "up-hit"
 hit.vec[ condtSample & condtDown ] = "down-hit"
 hit.vec[ condtSample & !condtUp & !condtDown] = "non-hit"
 result.df = cbind(HTSresults, "hitResult"=hit.vec)
 wells = as.character(unique(result.df[, "hitResult"])); wells
 colors = c("black",  "green", "white", "grey", "red",
            "purple1", "purple2", "yellow", "purple3")  
 par( mfrow=c(2,1) )
 imageDesign.fn(dataOnePlate.df=result.df[1:384,], wellName="hitResult",
                 rowName="XPOS", colName="YPOS", wells=wells, colors=colors,
                 title="Source Plate I")                
 imageDesign.fn(dataOnePlate.df=result.df[1:384+384,],wellName="hitResult",
                rowName="XPOS", colName="YPOS", wells=wells, colors=colors,
                 title="Source Plate II")