multiOmicsPlot_ORFikExp {RiboCrypt} | R Documentation |
Customizable html plots for visualizing genomic data.
multiOmicsPlot_ORFikExp( target_range, annotation = target_range, df, reference_sequence = findFa(df), reads = outputLibs(df, type = "pshifted", output.mode = "envirlist", naming = "full"), withFrames = libraryTypes(df, uniqueTypes = FALSE) %in% c("RFP", "RPF", "LSU"), frames_type = "lines", colors = NULL, kmers = NULL, kmers_type = c("mean", "sum")[1], ylabels = bamVarName(df), proportions = NULL, width = NULL, height = NULL, plot_name = "default", plot_title = NULL, display_sequence = FALSE, annotation_names = NULL, start_codons = "ATG", stop_codons = c("TAA", "TAG", "TGA"), custom_motif = NULL, BPPARAM = bpparam() )
target_range |
the whole region to visualize,
a |
annotation |
the whole annotation which your target region is a subset,
a |
df |
an ORFik |
reference_sequence |
the genome reference, default ORFik::findFa(df) |
reads |
the NGS libraries, as a list of |
withFrames |
a logical vector, default
|
frames_type |
character, default "lines". Alternative: |
colors |
character, default NULL (automatic colouring). If "withFrames" argument is TRUE, colors are set to to c("red", "green", "blue") for the 3 frames. Alternative: Character vector of length 1 or length of "reads" list argument. |
kmers |
numeric (integer), bin positions into kmers. |
kmers_type |
character, function used for kmers sliding window. default: "mean", alternative: "sum" |
ylabels |
character, default |
proportions |
numeric, default NULL. Width of plot. |
width |
numeric, default NULL. Width of plot. |
height |
numeric, default NULL. Height of plot. |
plot_name |
character, default "default" (will create name from target_range name). Alternative: custom name for region. |
plot_title |
character, default NULL. A title for plot. |
display_sequence |
logical, default FALSE. If TRUE, display nucleotide sequence in plot. |
annotation_names |
character, default NULL. Alternative naming for annotation. |
start_codons |
character vector, default "ATG" |
stop_codons |
character vector, default c("TAA", "TAG", "TGA") |
custom_motif |
character vector, default NULL. |
BPPARAM |
how many cores/threads to use? default: |
the plot object
library(ORFik) df <- ORFik.template.experiment()[3,] #Use third library in experiment only if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19")) { cds <- loadRegion(df, "cds") multiOmicsPlot_ORFikExp(extendLeaders(extendTrailers(cds[1], 30), 30), df = df, reference_sequence = BSgenome.Hsapiens.UCSC.hg19::Hsapiens, frames_type = "columns") }