## ----knitr-opts, include=FALSE------------------------------------------- knitr::opts_chunk$set(dpi = 90,dev = "png") ## ----install_logolas_bio, eval=FALSE------------------------------------- # source("http://bioconductor.org/biocLite.R") # biocLite("Logolas") ## ----install_logolas_git, eval=FALSE------------------------------------- # devtools::install_github('kkdey/Logolas') ## ----load, eval=TRUE----------------------------------------------------- library(Logolas) ## ----seq, cache=FALSE, eval=TRUE,warning=FALSE--------------------------- sequence <- c("CTATTGT", "CTCTTAT", "CTATTAA", "CTATTTA", "CTATTAT", "CTTGAAT", "CTTAGAT", "CTATTAA", "CTATTTA", "CTATTAT", "CTTTTAT", "CTATAGT", "CTATTTT", "CTTATAT", "CTATATT", "CTCATTT", "CTTATTT", "CAATAGT", "CATTTGA", "CTCTTAT", "CTATTAT", "CTTTTAT", "CTATAAT", "CTTAGGT", "CTATTGT", "CTCATGT", "CTATAGT", "CTCGTTA", "CTAGAAT", "CAATGGT") ## ----message = FALSE, warning = FALSE, fig.height=5, fig.width= 6, fig.align='center'---- logomaker(sequence, type = "Logo") logomaker(sequence, type = "EDLogo") ## ----message = FALSE, warning = FALSE, fig.height=5, fig.width= 6, fig.align='center'---- library(ggseqlogo) data(ggseqlogo_sample) sequence <- seqs_aa$AKT1 logomaker(sequence, type = "EDLogo") ## ------------------------------------------------------------------------ data("seqlogo_example") seqlogo_example ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- logomaker(seqlogo_example, type = "Logo", return_heights = TRUE) logomaker(seqlogo_example, type = "EDLogo", return_heights = TRUE) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- logomaker(seqlogo_example, color_type = "per_row", colors = c("#7FC97F", "#BEAED4", "#FDC086", "#386CB0"), type = "EDLogo") logomaker(seqlogo_example, type = "EDLogo", color_seed = 1500) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- logomaker(seqlogo_example, type = "Logo", logo_control = list(control = list(tofill= FALSE)), color_seed = 4000) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- logomaker(seqlogo_example, type = "EDLogo", logo_control = list(control = list(tofill_pos = TRUE, tofill_neg = FALSE))) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- bg <- c(0.05, 0.90, 0.03, 0.05) names(bg) <- c("A", "C", "G", "T") logomaker(seqlogo_example, bg=bg, type = "EDLogo") ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- logomaker(seqlogo_example, bg=(seqlogo_example+1e-02), type = "EDLogo") ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- sequence <- c("CTATTGT", "CTCTTAT", "CTATTAA", "CTATTTA", "CTATTAT", "CTTGAAT", "CTTAGAT", "CTATTAA", "CTATTTA", "CTATTAT") logomaker(sequence, use_dash = FALSE, type = "Logo", logo_control = list(pop_name = "use_dash = FALSE")) logomaker(sequence, type = "Logo", logo_control = list(pop_name = "use_dash = TRUE")) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- data("histone_marks") logomaker(histone_marks$mat, bg=histone_marks$bgmat, type = "EDLogo") ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- data("mutation_sig") logomaker(mutation_sig, type = "Logo", color_seed = 3000) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- logomaker(mutation_sig, type = "Logo", color_type = "per_symbol", color_seed = 2300) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- logomaker(mutation_sig, type = "EDLogo", color_type = "per_symbol", color_seed = 2300) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- sequence <- c("CTATTGT", "CTCTTAT", "CTATTAA", "CTATTTA", "CTATTAT", "CTTGAAT", "CTTAGAT", "CTATTAA", "CTATTTA", "CTATTAT") GetConsensusSeq(sequence) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- sequence <- c("CTATTGT", "CTCTTAT", "CTATTAA", "CTATTTA", "CTATTAT", "CTTGAAT", "CTTAGAT", "CTATTAA", "CTATTTA", "CTATTAT") Logolas::get_viewport_logo(1, 2, heights_1 = 20) library(grid) seekViewport(paste0("plotlogo", 1)) logomaker(sequence, type = "Logo", logo_control = list(newpage = FALSE)) seekViewport(paste0("plotlogo", 2)) logomaker(sequence, type = "EDLogo", logo_control = list(newpage = FALSE)) ## ----message = FALSE, warning=FALSE, fig.height=5, fig.width= 6, fig.align='center'---- data(pssm) logo_pssm(pssm, control = list(round_off = 0)) ## ------------------------------------------------------------------------ sessionInfo()