demo/test_logomaker.R

In Logolas: EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices

##############  test new logomaker   #######################

sequence <- c("CTATTGT", "CTCTTAT", "CTATTAA", "CTATTTA", "CTATTAT", "CTTGAAT",
              "CTTAGAT", "CTATTAA", "CTATTTA", "CTATTAT", "CTTTTAT", "CTATAGT",
              "CTATTTT", "CTTATAT", "CTATATT", "CTCATTT", "CTTATTT", "CAATAGT",
              "CATTTGA", "CTCTTAT", "CTATTAT", "CTTTTAT", "CTATAAT", "CTTAGGT",
              "CTATTGT", "CTCATGT", "CTATAGT", "CTCGTTA", "CTAGAAT", "CAATGGT")

logomaker(sequence, type = "Logo")
logomaker(sequence, type = "EDLogo")


counts_mat <- rbind(c(0, 10, 100, 60, 20),
                    c(40, 30, 30, 35, 20),
                    c(100, 0, 15, 25, 75),
                    c(10, 30, 20, 50, 70))
colnames(counts_mat) <- c("2012", "2013", "2014", "2015", "2016")
rownames(counts_mat) <- c("MAN", "MAIL", "LAWN", "CAR")

logomaker(counts_mat, type = "Logo")
logomaker(counts_mat, type = "EDLogo")

p <- get(load(system.file("extdata", "seqlogo_example.Rdata", package = "Logolas")))
logomaker(p, type = "Logo", return_heights = TRUE)
logomaker(p, type = "EDLogo", return_heights = TRUE)

logomaker(p, color_type = "per_row", colors = c("#7FC97F", "#BEAED4", "#FDC086", "#386CB0"), type = "Logo")
logomaker(p, color_type = "per_row", colors = c("#7FC97F", "#BEAED4", "#FDC086", "#386CB0"), type = "EDLogo")