Description Usage Arguments Author(s) References See Also Examples
View source: R/imageDesign.fn.R
A function that displays the image of well designs in a plate.
1 |
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. |
Xiaohua Douglas Zhang & Zhaozhi Zhang
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
imageIntensity.fn
, dualFlashlight.fn
,
plateWellSeries.fn
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 | # 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")
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