displayHTS (version 1.0)

displayHTS-package: Display high-throughput screening data and results

Description

An R package that displays data and results from high-throughput screening experiments.

Details

Package:

displayHTS

Type:

Package

Version:

1.0

Date:

2013-01-07

License:

GPL(>=2)

The R package displayHTS has four main functions for generating graphics to display data and results from HTS experiments: plateWellSeries.fn, imageDesign.fn, imageIntensity.fn, and dualFlashlight.fn. plateWellSeries.fn generates a scatter plot based on the measured or calculated values of each well in every plate in a HTS experiment. imageDesign.fn displays a plate design that can be used to both visualize the arrangement of controls and samples in a plate. imageIntensity.fn creates an image plot that shows the intensities or calculated values of every well utilizing the boxplot statistics and allows for easy analysis of any systematic errors of measurement; finally, dualFlashlight.fn generates the dual-flashlight plot, volcano plot and plate correlation plot. This package also includes three example datasets: HTSdata, HTSdataSort and HTSresults. HTSdata contain the raw data; after sorting and removing redundant records, the data are stored into HTSdataSort. Finally, the data are processed and the SSMD, mean, p-value, and number of replicates of the data are contained in the dataset HTSresults.

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, Santini F, Lacson R, Marine SD, Wu Q, Benetti L, Yang R, McCampbell A, Berger JP, Toolan DM, Stec EM, Holder DJ, Soper KA, Heyse JF and Ferrer M. 2011. cSSMD: Assessing collective activity of multiple siRNAs in genome-scale RNAi screens. Bioinformatics 27(20): 2775-2781.

Zhang XHD. 2011. Illustration of SSMD, z-score, SSMD*, z*-score and t-statistic for hit selection in high-throughput screens. Journal of Biomolecular Screening 16 (7): 775 - 785.

Zhang XHD. 2010. Assessing the size of gene or RNAi effects in multi-factor high-throughput experiments. Pharmacogenomics 11(2): 199 - 213.

Zhang XHD. 2009. A method effectively comparing gene effects in multiple conditions in RNAi and expression profiling research. Pharmacogenomics 10(3):345-358.

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.

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. 2007. A new method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high throughput screening assays. Journal of Biomolecular Screening 12 (5): 645-655.

Zhang XHD, Ferrer M, Espeseth AS, Marine SD, Stec EM, Crackower MA, Holder DJ, Heyse JF, Strulovici B. 2007. The use of strictly standardized mean difference for hit selection in primary RNA interference high throughput screening experiments. Journal of Biomolecular Screening 12 (4): 497-509.

Zhang XHD. 2007. A pair of new statistical parameters for quality control in RNA interference high throughput screening assays. Genomics 39: 552-561.

Zhang XHD, Yang XC, Chung N, Gates AT, Stec EM, Kunapuli P, Holder DJ, Ferrer M, Espeseth AS. 2006. Robust statistical methods for hit selection in RNA interference high throughput screening experiments. Pharmacogenomics 7 (3) 299-309.

Examples

#######################################################################
## generate the figures in the article where this package is published
#######################################################################
# fig1.A: plate-well series plot
data(HTSdataSort)
wells = as.character(unique(HTSdataSort[, "WELL_USAGE"]))
colors = c("black",  "pink", "grey", "blue", "skyblue", "green", "red")
orders=c(1, 3, 2, 4, 5, 7, 6)
par( mfrow=c(1,1) )                                                        
plateWellSeries.fn(data.df = HTSdataSort[1:(384*2),],
                   intensityName="log2Intensity",       
                   plateName="BARCODE", wellName="WELL_USAGE",              
                   rowName="XPOS", colName="YPOS", show.wellTypes=wells,     
                   order.wellTypes=orders, color.wells=colors,
                   pch.wells=rep(1, 7), ppf=6, byRow=TRUE,
                   yRange=NULL, cex.point=0.75,cex.legend=0.75,
                   main="A: Plate-well series plot") 

# fig1.B: 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", "red",
           "grey", "purple1", "purple2", "pink", "purple3")  
par( mfrow=c(1,1) )
imageDesign.fn(result.df[1:384,], wellName="hitResult", rowName="XPOS",
                colName="YPOS", wells=wells, colors=colors,
                title="B: Image of hits and controls")    

## fig1.C: dual-flashlight plot,
par( mfrow=c(1, 1) )
dualFlashlight.fn(HTSresults, wellName="WELL_USAGE", x.name="mean",
                  y.name="ssmd", sampleName="Sample", sampleColor="black", 
                  controls = c("negCTRL", "posCTRL1", "mock1"),
                  controlColors = c("green", "red", "lightblue"), 
                  xlab="Average Fold Change", ylab="SSMD",
                  main="C: Dual-Flashlight Plot", x.legend=0.1, y.legend= -12, 
                  cex.point=1, cex.legend = 0.8,
                  xat=log2( c(1/4, 1/2, 1/1.2, 1, 1.2, 2, 4) ), 
                  xMark=c("1/4", "1/2", "1/1.2","1", "1.2", "2", "4"),
                  xLines=log2( c(1/4, 1/2, 1/1.2, 1, 1.2, 2, 4) ),
                  yLines=c(-5, -3, -2, -1, 0, 1, 2, 3, 5 ) )

## fig1.D: volcano plot,
result.df = cbind(HTSresults, "neg.log10.pval" = -log10(HTSresults[,"p.value"]))
dualFlashlight.fn(result.df, wellName="WELL_USAGE", x.name="mean",
                  y.name="neg.log10.pval",
                  sampleName="Sample", sampleColor="black", 
                  controls = c("negCTRL", "posCTRL1", "mock1"),
                  controlColors = c("green", "red", "lightblue"), 
                  xlab="Average Fold Change", ylab="p-value in -log10 scale",
                  main="D: Volcano Plot", x.legend=NA, y.legend=-log10(0.006), 
                  cex.point=1, cex.legend = 0.8,
                  xat=log2( c(1/4, 1/2, 1/1.2, 1, 1.2, 2, 4) ), 
                  xMark=c("1/4", "1/2", "1/1.2","1", "1.2", "2", "4"),
                  xLines=log2( c(1/4, 1/2, 1/1.2, 1, 1.2, 2, 4) ),
                  yLines=c(-5, -3, -2, -1, 0, 1, 2, 3, 5 ) )