View source: R/browser_default.R
multiOmicsPlot_list | R Documentation |
Customizable html plots for visualizing genomic data.
multiOmicsPlot_list(
display_range,
annotation = display_range,
reference_sequence,
reads,
viewMode = c("tx", "genomic")[1],
custom_regions = NULL,
leader_extension = 0,
trailer_extension = 0,
withFrames = NULL,
frames_type = "lines",
colors = NULL,
kmers = NULL,
kmers_type = c("mean", "sum")[1],
ylabels = NULL,
lib_to_annotation_proportions = c(0.8, 0.2),
lib_proportions = NULL,
annotation_proportions = NULL,
width = NULL,
height = NULL,
plot_name = "default",
plot_title = NULL,
display_sequence = c("both", "nt", "aa", "none")[1],
seq_render_dist = 100,
aa_letter_code = c("one_letter", "three_letters")[1],
annotation_names = NULL,
start_codons = "ATG",
stop_codons = c("TAA", "TAG", "TGA"),
custom_motif = NULL,
AA_code = Biostrings::GENETIC_CODE,
log_scale = FALSE,
BPPARAM = BiocParallel::SerialParam(),
summary_track = FALSE,
summary_track_type = frames_type,
export.format = "svg"
)
display_range |
the whole region to visualize,
a |
annotation |
the whole annotation which your target region is a subset,
a |
reference_sequence |
the genome reference,
a |
reads |
the NGS libraries, as a list of |
viewMode |
character, default "tx" (transcript coordinates, first position is 1,
exons are merged into a single sequence) |
custom_regions |
a GRangesList or NULL, default: NULL. The alternative annotation, like self defined uORFs etc. The vertical annotation bars will have a different color. |
leader_extension |
integer, default 0. (How much to extend view upstream) |
trailer_extension |
integer, default 0. (How much to extend view downstream) |
withFrames |
a logical vector, default NULL. Alternative: a length 1 or same length as list length of "reads" argument. |
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 NULL. Name of libraries in "reads" list arugment. |
lib_to_annotation_proportions |
numeric vector of length 2. relative sizes of profiles and annotation. |
lib_proportions |
numeric vector of length equal to displayed libs. Relative sizes of profiles displayed |
annotation_proportions |
numeric vector of length 3 (seq displayed), or 2 (seq not displayed). Relative sizes of annotation tracks. |
width |
numeric, default NULL. Width of plot. |
height |
numeric, default NULL. Height of plot. |
plot_name |
= character, default "default" (will create name from display_range name). Alternative: custom name for region. |
plot_title |
character, default NULL. A title for plot. |
display_sequence |
character/logical, default |
seq_render_dist |
integer, default 100. The sequences will appear after zooming below this threshold. |
aa_letter_code |
character, when set to "three_letters", three letter amino acid code is used. One letter by default. |
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. |
AA_code |
Genetic code for amino acid display. Default is SGC0 (standard: Vertebrate).
See |
log_scale |
logical, default FALSE. Log2 scale the count values, for easier visualization of shapes. |
BPPARAM |
how many cores/threads to use? default: |
summary_track |
logical, default FALSE. Display a top track, that is the sum of all tracks. |
summary_track_type |
character, default is same as 'frames_type' argument |
export.format |
character, default: "svg". alternative: "png". when you click the top right image button export, what should it export as? |
the plot object
library(RiboCrypt)
df <- ORFik.template.experiment()[9:10,]
cds <- loadRegion(df, "cds")
mrna <- loadRegion(df, "mrna")
multiOmicsPlot_list(mrna[1], annotation = cds[1], reference_sequence = findFa(df),
frames_type = "columns", leader_extension = 30, trailer_extension = 30,
reads = outputLibs(df, type = "pshifted", output.mode = "envirlist",
naming = "full", BPPARAM = BiocParallel::SerialParam()))
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