barcodeplot(statistics, index = NULL, index2 = NULL, gene.weights = NULL, weights.label = "Weight", labels = c("Up","Down"), quantiles = c(-1,1)*sqrt(2), col.bars = NULL, alpha = 0.4, worm = TRUE, span.worm=0.45, ...)statistics or, in general, any vector such that statistic[index] gives a subset of the statistic values.
Can be omitted if gene.weights has same length as statistics, in which case positive values of gene.weights indicate to members of the positive set and negative weights correspond to members of the negative set.index and index2 specify positive and negative genes respectively.
Usually used to distinguish down-regulated genes from up-regulated genes.index2 is non-null.gene.weights.statistics considered small or large respectively. Used to color the rectangle of the barcodeplot."black" for one set or c("red","blue") for two sets.gene.weights are not NULL, values 0 give semitransparent colors for the vertical bars inside the rectangle. This helps distinguish position bars from the weighted bars and also helps to show the density of the bars when there are many bars. Ignored if gene.weights=NULL. plot.The statistics are ranked left to right from largest to smallest. The ranked statistics are represented by a shaded bar or bed, and the positions of the specified subsets are marked by vertical bars, forming a pattern like a barcode. An enrichment worm optionally shows the relative enrichment of the vertical bars in each part of the plot.
Barcode plots are often used in conjunction with gene set tests, and show the enrichment of gene sets amongst high or low ranked genes. They were inspired by the set location plot of Subramanian et al (2005), with a number of enhancements, especially the ability to plot positive and negative sets simultaneously. Barcode plots first appeared in the literature in Lim et al (2009). More recent examples can be seen in Liu et al (2014), Sheikh et al (2015), Witkowski et al (2015) and Ng et al (2015).
The function can be used with any of four different calling sequences:
index is specified, but not index2 or gene.weights. Single direction plot.
index and index2 are specified. Two directional plot.
index and gene.weights are specified. gene.weights must have same length as statistics[index]. Plot will be two-directional if gene.weights contains positive and negative values.
gene.weights is specified by not index or index2. gene.weights must have same length as statistics. Plot will be two-directional if gene.weights contains positive and negative values.
Lim E, Vaillant F, Wu D, Forrest NC, Pal B, Hart AH, Asselin-Labat ML, Gyorki DE, Ward T, Partanen A, Feleppa F, Huschtscha LI, Thorne HJ; kConFab; Fox SB, Yan M, French JD, Brown MA, Smyth GK, Visvader JE, and Lindeman GJ (2009). Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nat Med, 15, 907-913.
Liu, GJ, Cimmino, L, Jude, JG, Hu, Y, Witkowski, MT, McKenzie, MD, Kartal-Kaess, M, Best, SA, Tuohey, L, Liao, Y, Shi, W, Mullighan, CG, Farrar, MA, Nutt, SL, Smyth, GK, Zuber, J, and Dickins, RA (2014). Pax5 loss imposes a reversible differentiation block in B progenitor acute lymphoblastic leukemia. Genes & Development 28, 1337-1350. http://www.ncbi.nlm.nih.gov/pubmed/24939936
Sheikh, B, Lee, S, El-saafin, F, Vanyai, H, Hu, Y, Pang, SHM, Grabow, S, Strasser, A, Nutt, SL, Alexander, WS, Smyth, GK, Voss, AK, and Thomas, T (2015). MOZ regulates B cell progenitors in mice, consequently, Moz haploinsufficiency dramatically retards MYC-induced lymphoma development. Blood, 125, 1910-1921. http://www.ncbi.nlm.nih.gov/pubmed/25605372
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, and Mesirov JP (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA, 102, 15545-15550.
Witkowski, MT, Cimmino, L, Hu, Y, Trimarchi, T, Tagoh, H, McKenzie, MD, Best, SA, Tuohey, L, Willson, TA, Nutt, SL, Meinrad Busslinger, M, Aifantis, I, Smyth, GK, and Dickins, RA (2015). Activated Notch counteracts Ikaros tumor suppression in mouse and human T cell acute lymphoblastic leukemia. Leukemia. http://www.ncbi.nlm.nih.gov/pubmed/25655195
tricubeMovingAverage, roast, camera, romer, geneSetTestThere is a topic page on 10.GeneSetTests.
stat <- rnorm(100)
sel <- 1:10
sel2 <- 11:20
stat[sel] <- stat[sel]+1
stat[sel2] <- stat[sel2]-1
# One directional
barcodeplot(stat, index = sel)
# Two directional
barcodeplot(stat, index = sel, index2 = sel2)
# Second set can be indicated by negative weights
barcodeplot(stat, index = c(sel,sel2), gene.weights = c(rep(1,10), rep(-1,10)))
# Two directional with unequal weights
w <- rep(0,100)
w[sel] <- runif(10)
w[sel2] <- -runif(10)
barcodeplot(stat, gene.weights = w, weights.label = "logFC")
# One directional with unequal weights
w <- rep(0,100)
w[sel2] <- -runif(10)
barcodeplot(stat, gene.weights = w, weights.label = "logFC", col.bars = "dodgerblue")
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