inst/doc/Logolas.R

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

## ----knitr-opts, include=FALSE-------------------------------------------
knitr::opts_chunk$set(dpi = 90,dev = "png")

## ----install_logolas_bio, eval=FALSE-------------------------------------
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("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()