limma (version 3.28.6)

barcodeplot: Barcode Enrichment Plot

Description

Display the enrichment of one or two gene sets in a ranked gene list.

Usage

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, ...)

Arguments

statistics

numeric vector giving the values of statistics to rank genes by.

index

index vector for the gene set. This can be a vector of indices, or a logical vector of the same length as 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.

index2

optional index vector for a second (negative) gene set. If specified, then index and index2 specify positive and negative genes respectively. Usually used to distinguish down-regulated genes from up-regulated genes.

gene.weights

numeric vector giving directional weights for the genes in the (first) set. Positive and negative weights correspond to positive and negative genes. Ignored if index2 is non-null.

weights.label

label describing the entries in gene.weights.

labels

character vector of labels for high and low statistics. First label is associated with high statistics and is displayed at the left end of the plot. Second label is associated with low or negative statistics and is displayed at the right end of the plot.

quantiles

numeric vector of length 2, giving cutoff values for statistics considered small or large respectively. Used to color the rectangle of the barcodeplot.

col.bars

character vector of colors for the vertical bars of the barcodeplot showing the ranks of the gene set members. Defaults to "black" for one set or c("red","blue") for two sets.

alpha

transparency for vertical bars. When 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.

worm

logical, should enrichment worms be plotted?

span.worm

loess span for enrichment worms. Larger spans give smoother worms.

...

other arguments are passed to plot.

Value

• No value is returned but a plot is produced as a side effect.

Details

This function plots the positions of one or two gene sets in a ranked list of statistics. If there are two sets, then one is considered to be the positive set and the other the down set. For example, the first set and second sets often correspond to genes that are expected to be up- or down-regulated respectively. The function can optionally display varying weights for different genes, for example log-fold-changes from a previous experiment. 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:

• indexis specified, but notindex2orgene.weights. Single direction plot.
• indexandindex2are specified. Two directional plot.
• indexandgene.weightsare specified.gene.weightsmust have same length asstatistics[index]. Plot will be two-directional ifgene.weightscontains positive and negative values.
• gene.weightsis specified by notindexorindex2.gene.weightsmust have same length asstatistics. Plot will be two-directional ifgene.weightscontains positive and negative values.

References

Ng, AP, Hu, Y, Metcalf, D, Hyland, CD, Ierino, H, Phipson, B, Wu, D, Baldwin, TM, Kauppi, M, Kiu, H, Di, Rago, L, Hilton, DJ, Smyth, GK, Alexander, WS (2015). Early lineage priming by trisomy of Erg leads to myeloproliferation in a down syndrome model. PLOS Genetics 11, e1005211. http://www.ncbi.nlm.nih.gov/pubmed/25973911 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

See Also

tricubeMovingAverage, roast, camera, romer, geneSetTest There is a topic page on 10.GeneSetTests.

Examples

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")