Package 'RiboCrypt'

Browse a gene on Ribocrypt webpage

Description

Can also disply local RiboCrypt app

Usage

browseRC(
  symbol = NULL,
  gene_id = NULL,
  tx_id = NULL,
  exp = "all_merged-Homo_sapiens_modalities",
  libraries = NULL,
  leader_extension = 0,
  trailer_extension = 0,
  viewMode = FALSE,
  other_tx = FALSE,
  plot_on_start = TRUE,
  frames_type = "columns",
  kmer = 1,
  host = "https://ribocrypt.org",
  browser = getOption("browser")
)

Arguments

symbol	gene symbol, default NULL
gene_id	gene symbol, default NULL
tx_id	gene symbol, default NULL
exp	experiment name, default "all_merged-Homo_sapiens_modalities"
libraries	NULL, default to first in experiment, c("RFP","RNA") would add RNA to default.
leader_extension	integer, default 0. (How much to extend view upstream)
trailer_extension	integer, default 0. (How much to extend view downstream)
viewMode	FALSE (transcript view), TRUE gives genomic.
other_tx	FALSE, show all other annotation in region (isoforms etc.)
plot_on_start	logical, default TRUE. Plot gene when opening browser.
frames_type	"columns"
kmer	integer, default 1 (no binning), binning size of windows, to smear out the signal.
host	url, default "https://ribocrypt.org". Set to localhost for local version.
browser	getOption("browser")

Value

browseURL, opens browse with page

Examples

browseRC("ATF4", "ENSG00000128272")

---

Get collection directory

Description

Get collection directory

Usage

collection_dir_from_exp(df, must_exists = FALSE)

Arguments

df	ORFik experiment
must_exists	logical, stop if dir does not exists

Value

file.path(resFolder(df), "collection_tables")

Examples

df <- ORFik.template.experiment()
collection_dir_from_exp(df)

---

Get collection path

Description

For directory and id, must be fst format file

Usage

collection_path_from_exp(
  df,
  id,
  gene_name_list = NULL,
  must_exists = TRUE,
  collection_dir = collection_dir_from_exp(df, must_exists)
)

Arguments

df	ORFik experiment
id	character, transcript ids
gene_name_list	a data.table, default NULL, with gene ids
must_exists	logical, stop if dir does not exists
collection_dir	= collection_dir_from_exp(df, must_exists)

Value

file.path(resFolder(df), "collection_tables")

Examples

df <- ORFik.template.experiment()
tx_id <- "ENST0000012312"
collection_path_from_exp(df, id = tx_id, must_exists = FALSE)

---

Cast a collection table to wide format

Description

Cast a collection table to wide format

Usage

collection_to_wide(table, value.var = "logscore")

Arguments

table	a data.table in long format
value.var	which column to use as scores, default "logscore"

Value

a table in wide format

---

Get collection table normalized in wide format

Description

Get collection table normalized in wide format

Usage

compute_collection_table(
  path,
  lib_sizes,
  df,
  metadata_field,
  normalization,
  kmer,
  metadata,
  min_count = 0,
  format = "wide",
  value.var = "logscore",
  as_list = FALSE,
  subset = NULL,
  group_on_tx_tpm = NULL,
  split_by_frame = FALSE,
  ratio_interval = NULL,
  decreasing_order = FALSE
)

Arguments

path	the path to gene counts
lib_sizes	named integer vector, default NULL. If given will do a pre tpm normalization for full library sizes
df	the ORFik experiment to load the precomputed collection from. It must also have defined runIDs() for all samples.
metadata_field	the column name in metadata, to select to group on.
normalization	a character string, which mode, for options see RiboCrypt:::normalizations
kmer	integer, default 1L (off), if > 1 will smooth out signal with sliding window size kmer.
metadata	a data.table of metadata, must contain the Run column to select libraries.
min_count	integer, default 0. Minimum counts of coverage over transcript to be included.
format	character, default "wide", alternative "long". The format of the table output.
value.var	which column to use as scores, default "logscore"
as_list	logical, default FALSE. Return as list of size 2, count data.table and metadata data.table Set to TRUE if you need metadata subset (needed if you subset the table, to get correct matching)
subset	numeric vector, positional interval to subset, must be <= size of whole region.
group_on_tx_tpm	numeric vector, default NULL. tpm values per libraries. Either for that gene or some other gene.
split_by_frame	logical, default FALSE For kmer sliding window, should it split by frame
ratio_interval	numeric vector of size 2 or 4, default NULL. If 2, means you should sort libraries on coverage in that region. If 4, means to sort on ratio of that region in this gene vs the other region in another gene.

Value

a data.table in long or wide (default) format, if as list, it is a list of size 2 (see argument as_list)

---

Differential expression plots (1D or 2D)

Description

Gives you interactive 1D or 2D DE plots

Usage

DEG_plot(
  dt,
  draw_non_regulated = FALSE,
  xlim = ifelse(two_dimensions, "bidir.max", "auto"),
  ylim = "bidir.max",
  xlab = ifelse(two_dimensions, "RNA fold change (log2)", "Mean counts (log2)"),
  ylab = ifelse(two_dimensions, "RFP fold change (log2)", "Fold change (log2)"),
  two_dimensions = ifelse("LFC" %in% colnames(dt), FALSE, TRUE),
  color.values = c(`No change` = "black", Significant = "red", Buffering = "purple",
    `mRNA abundance` = "darkgreen", Expression = "blue", Forwarded = "yellow", Inverse =
    "aquamarine", Translation = "orange4")
)

Arguments

dt	a data.table with results from a differential expression run. Normally from: ORFik::DTEG.analysis(df1, df2)
draw_non_regulated	logical, default FALSE. Should non-regulated rows be included in the plot? Will make the plot faster to render if skipped (FALSE)
xlim	numeric vector or character preset, default: ifelse(two_dimensions, "bidir.max", "auto") (Equal in both + / - direction, using max value + 0.5 of meanCounts(in 1d) / rna(in 2d) column of dt). If you want ggplot to decide limit, set to "auto". For numeric vector, specify min and max x limit: like c(-5, 5)
ylim	numeric vector or character preset, default: "bidir.max" (Equal in both + / - direction, using max value + 0.5 of LFC(in 1d) / rfp(in 2d) column of dt). If you want ggplot to decide limit, set to "auto". For numeric vector, specify min and max x limit: like c(-5, 5)
xlab	character, default: ifelse(two_dimensions, "RNA fold change (log2)", "Mean counts (log2)")
ylab	character, default: ifelse(two_dimensions, "RFP fold change (log2)", "Fold change (log2)")
two_dimensions	logical, default: ifelse("LFC" %in% colnames(dt), FALSE, TRUE) Is this two dimensional, like: Ribo-seq vs RNA-seq. Alternative, FALSE: Then Log fold change vs mean counts
color.values	named character vector, default: c("No change" = "black", "Significant" = "red", "Buffering" = "purple", "mRNA abundance" = "darkgreen", "Expression" = "blue", "Forwarded" = "yellow", "Inverse" = "aquamarine", "Translation" = "orange4")

Value

plotly object

Examples

# Load experiment
df <- ORFik.template.experiment()
df_rna <- df[df$libtype == "RNA",]
# 1 Dimensional analysis
dt <- DEG.analysis(df_rna)
dt$Regulation[1] <- "Significant" # Fake sig level
DEG_plot(dt, draw_non_regulated = TRUE)
# 2 Dimensional analysis
df_rfp <- df[df$libtype == "RFP",]
dt_2d <- DTEG.analysis(df_rfp, df_rna, output.dir = NULL)
dt_2d$Regulation[4] <- "Translation" # Fake sig level
dt_2d$rfp.lfc[4] <- -0.3 # Fake sig level
dt_2d$Regulation[5] <- "Buffering" # Fake sig level
dt_2d$rna.lfc[5] <- -0.3 # Fake sig level
DEG_plot(dt_2d, draw_non_regulated = TRUE)

---

Fetch Javascript sequence

Description

Fetch Javascript sequence

Usage

fetch_JS_seq(
  target_seq,
  nplots,
  distance = 50,
  display_dist,
  aa_letter_code = "one_letter"
)

Arguments

target_seq	the target sequence
nplots	number of plots
distance	numeric, default 50.
display_dist	display distance
aa_letter_code	"one_letter"

Value

a list of 2 lists, the nt list (per frame, total 3) and AA list (per frame, total 3)

---

Fetch summary of uniprot id

Description

Fetch summary of uniprot id

Usage

fetch_summary(qualifier, provider = "alphafold")

Arguments

qualifier	uniprot ids
provider	"pdbe", alternatives: "alphafold", "all"

Value

a character of json

---

Full plot for allsamples browser

Description

Full plot for allsamples browser

Usage

get_meta_browser_plot_full(
  m,
  heatmap,
  id,
  df,
  summary = TRUE,
  annotation = TRUE,
  region_type,
  rel_heights = c(0.2, 0.75, 0.05)
)

Arguments

m	data.table of coverage per sample (wide format)
heatmap	ComplexHeatmap object of plot from 'm'
id	id of transcript
df	ORFik experiment
summary	logical, default TRUE (add top plot)
annotation	logical, default TRUE (add bottom annotation track)
region_type	character, "what is the coverage region?" Usually full mrna: "mrna" or "leader+cds".
rel_heights	numeric < 1, default: c(0.2, 0.75, 0.05). Relative heights, sum to 1 and must be length 3.

Value

a cowplot grub

---

Load a ORFik collection table

Description

Load a ORFik collection table

Usage

load_collection(path)

Arguments

path	the path to gene counts

Value

a data.table in long format

---

Create URL to browse a gene on Ribocrypt webpage

Description

Can also make url for local RiboCrypt app' On the actuall app, the function make_url_from_inputs is used on the shiny reactive input object. This one is for manual use.

Usage

make_rc_url(
  symbol = NULL,
  gene_id = NULL,
  tx_id = NULL,
  exp = "all_merged-Homo_sapiens_modalities",
  libraries = NULL,
  leader_extension = 0,
  trailer_extension = 0,
  viewMode = FALSE,
  other_tx = FALSE,
  plot_on_start = TRUE,
  frames_type = "columns",
  kmer = 1,
  add_translons = FALSE,
  zoom_range = NULL,
  host = "https://ribocrypt.org"
)

Arguments

symbol	gene symbol, default NULL
gene_id	gene symbol, default NULL
tx_id	gene symbol, default NULL
exp	experiment name, default "all_merged-Homo_sapiens_modalities"
libraries	NULL, default to first in experiment, c("RFP","RNA") would add RNA to default.
leader_extension	integer, default 0. (How much to extend view upstream)
trailer_extension	integer, default 0. (How much to extend view downstream)
viewMode	FALSE (transcript view), TRUE gives genomic.
other_tx	FALSE, show all other annotation in region (isoforms etc.)
plot_on_start	logical, default TRUE. Plot gene when opening browser.
frames_type	"columns"
kmer	integer, default 1 (no binning), binning size of windows, to smear out the signal.
zoom_range	character, zoom values.
host	url, default "https://ribocrypt.org". Set to localhost for local version.

Value

character, URL.

Examples

make_rc_url("ATF4", "ENSG00000128272")

---

Multi-omics animation using list input

Description

The animation will move with a play butten, there is 1 transition per library given.

Usage

multiOmicsPlot_animate(
  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",
  frames_subset = "all"
)

Arguments

display_range	the whole region to visualize, a GRangesList or GRanges object
annotation	the whole annotation which your target region is a subset, a GRangesList or GRanges object
reference_sequence	the genome reference, a FaFile or FaFile convertible object
reads	the NGS libraries, as a list of GRanges with or without score column for replicates.
viewMode	character, default "tx" (transcript coordinates, first position is 1, exons are merged into a single sequence) Alternative: "genomic" (genomic coordinates, first position is first position in display_range argument. Introns are displayed).
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: - columns - stacks - area
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. Default NULL, which is equal to 1, i.e. no binning.
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 c("both","nt", "aa", "none")[1]. If TRUE or "both", display nucleotide and aa sequence in plot.
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 Biostrings::GENETIC_CODE_TABLE for options. To change to bacterial, do: Biostrings::getGeneticCode("11")
log_scale	logical, default FALSE. Log2 scale the count values, for easier visualization of shapes.
BPPARAM	how many cores/threads to use? default: BiocParallel::SerialParam(). To see number of threads used for multicores, do BiocParallel::bpparam()$workers. You can also add a time remaining bar, for a more detailed pipeline.
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?
frames_subset	character, default "all". Alternatives: "red", "green", "blue".

Value

the plot object

Examples

library(RiboCrypt)
df <- ORFik.template.experiment()[9:10,]
cds <- loadRegion(df, "cds")
mrna <- loadRegion(df, "mrna")
multiOmicsPlot_animate(mrna[1], annotation = cds[1], reference_sequence = findFa(df),
                    frames_type = "columns", leader_extension = 30, trailer_extension = 30, withFrames = c(T, T),
                    reads = outputLibs(df, type = "pshifted", output.mode = "envirlist",
                                  naming = "full", BPPARAM = BiocParallel::SerialParam()))

---

Multi-omics plot using list input

Description

Customizable html plots for visualizing genomic data.

Usage

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",
  frames_subset = "all"
)

Arguments

display_range	the whole region to visualize, a GRangesList or GRanges object
annotation	the whole annotation which your target region is a subset, a GRangesList or GRanges object
reference_sequence	the genome reference, a FaFile or FaFile convertible object
reads	the NGS libraries, as a list of GRanges with or without score column for replicates.
viewMode	character, default "tx" (transcript coordinates, first position is 1, exons are merged into a single sequence) Alternative: "genomic" (genomic coordinates, first position is first position in display_range argument. Introns are displayed).
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: - columns - stacks - area
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. Default NULL, which is equal to 1, i.e. no binning.
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 c("both","nt", "aa", "none")[1]. If TRUE or "both", display nucleotide and aa sequence in plot.
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 Biostrings::GENETIC_CODE_TABLE for options. To change to bacterial, do: Biostrings::getGeneticCode("11")
log_scale	logical, default FALSE. Log2 scale the count values, for easier visualization of shapes.
BPPARAM	how many cores/threads to use? default: BiocParallel::SerialParam(). To see number of threads used for multicores, do BiocParallel::bpparam()$workers. You can also add a time remaining bar, for a more detailed pipeline.
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?
frames_subset	character, default "all". Alternatives: "red", "green", "blue".

Value

the plot object

Examples

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()))

---

Multi-omics plot using ORFik experiment input

Description

Customizable html plots for visualizing genomic data.

Usage

multiOmicsPlot_ORFikExp(
  display_range,
  df,
  annotation = "cds",
  reference_sequence = findFa(df),
  reads = outputLibs(df, type = "pshifted", output.mode = "envirlist", naming = "full",
    BPPARAM = BiocParallel::SerialParam()),
  viewMode = c("tx", "genomic")[1],
  custom_regions = NULL,
  leader_extension = 0,
  trailer_extension = 0,
  withFrames = libraryTypes(df, uniqueTypes = FALSE) %in% c("RFP", "RPF", "LSU", "TI"),
  frames_type = "lines",
  colors = NULL,
  kmers = NULL,
  kmers_type = c("mean", "sum")[1],
  ylabels = bamVarName(df),
  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,
  log_scale = FALSE,
  BPPARAM = BiocParallel::SerialParam(),
  input_id = "",
  summary_track = FALSE,
  summary_track_type = frames_type,
  export.format = "svg",
  frames_subset = "all"
)

Arguments

display_range	the whole region to visualize, a GRangesList or GRanges object
df	an ORFik experiment or a list containing ORFik experiments. Usually a list when you have split Ribo-seq and RNA-seq etc.
annotation	the whole annotation which your target region is a subset, a GRangesList or GRanges object
reference_sequence	the genome reference, default ORFik::findFa(df)
reads	the NGS libraries, as a list of GRanges with or without 'score' column for replicates. Can also be a covRle object of precomputed coverage. Default: outputLibs(df, type = "pshifted", output.mode = "envirlist", naming = "full", BPPARAM = BiocParallel::SerialParam())
viewMode	character, default "tx" (transcript coordinates, first position is 1, exons are merged into a single sequence) Alternative: "genomic" (genomic coordinates, first position is first position in display_range argument. Introns are displayed).
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 libraryTypes(df, uniqueTypes = FALSE) %in% c("RFP", "RPF", "LSU", "TI") Alternative: a length 1 or same length as list length of "reads" argument.
frames_type	character, default "lines". Alternative: - columns - stacks - area
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. Default NULL, which is equal to 1, i.e. no binning.
kmers_type	character, function used for kmers sliding window. default: "mean", alternative: "sum"
ylabels	character, default bamVarName(df). Name of libraries in "reads" list argument.
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).
plot_title	character, default NULL. A title for plot.
display_sequence	character/logical, default c("both","nt", "aa", "none")[1]. If TRUE or "both", display nucleotide and aa sequence in plot.
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.
log_scale	logical, default FALSE. Log2 scale the count values, for easier visualization of shapes.
BPPARAM	how many cores/threads to use? default: BiocParallel::SerialParam(). To see number of threads used for multicores, do BiocParallel::bpparam()$workers. You can also add a time remaining bar, for a more detailed pipeline.
input_id	character path, default: "", id for shiny to disply structures, should be "" for local users.
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?
frames_subset	character, default "all". Alternatives: "red", "green", "blue".

Value

the plot object

Examples

library(RiboCrypt)
df <- ORFik.template.experiment()[9,] #Use third library in experiment only
cds <- loadRegion(df, "cds")
multiOmicsPlot_ORFikExp(extendLeaders(extendTrailers(cds[1], 30), 30), df,
                        frames_type = "columns")

---

Normalize collection table

Description

Normalize collection table

Usage

normalize_collection(
  table,
  normalization,
  lib_sizes = NULL,
  kmer = 1L,
  add_logscore = TRUE,
  split_by_frame = FALSE
)

Arguments

table	a data.table in long format
normalization	a character string, which mode, for options see RiboCrypt:::normalizations
lib_sizes	named integer vector, default NULL. If given will do a pre tpm normalization for full library sizes
kmer	integer, default 1L (off), if > 1 will smooth out signal with sliding window size kmer.
add_logscore	logical, default TRUE, adds a log(score + 1) to table
split_by_frame	logical, default FALSE For kmer sliding window, should it split by frame

Value

a data.table of normalized results

---

Select box for organism

Description

Select box for organism

Usage

organism_input_select(genomes, ns)

Arguments

genomes	name of genomes, returned from list.experiments()
ns	the ID, for shiny session

Value

selectizeInput object

---

Create RiboCrypt app

Description

Create RiboCrypt app

Usage

RiboCrypt_app(
  validate.experiments = TRUE,
  options = list(launch.browser = ifelse(interactive(), TRUE, FALSE)),
  all_exp = list.experiments(validate = validate.experiments),
  browser_options = c(),
  init_tab_focus = "browser",
  metadata = NULL,
  all_exp_meta = all_exp[grep("all_samples-", name), ]
)

Arguments

validate.experiments	logical, default TRUE, set to FALSE to allow starting the app with malformed experiments, be careful will crash if you try to load that experiment!
options	list of arguments, default list("launch.browser" = ifelse(interactive(), TRUE, FALSE))
all_exp	a data.table, default: list.experiments(validate = validate.experiments). Which experiments do you want to allow your app to see, default is all in your system config path.
browser_options	named character vector of browser specific arguments: - default_experiment : Which experiment to select, default: first one - default_gene : Which genes to select, default: first one - default_isoform : Which isoform to select, default: first one - default_libs : Which libraries to select: first one, else a single string, where libs are seperated by "|", like "RFP_WT_r1|RFP_WT_r2". - default_kmer : K-mer windowing size, default: 1 - default_frame_type : Ribo-seq line type, default: "lines" - default_view_mode : "tx", alternative "genomic" - plot_on_start : Plot when starting, default: "FALSE"
init_tab_focus	character, default "browser". Which tab to open on init.
metadata	a path to csv or a data.table of metadata columns, must contain a "Run" column to merge IDs to ORFik experiments. It is used in the metabrowser tab for grouping of samples.
all_exp_meta	a data.table, default: all_exp[grep("all_samples-", name),]. Can also be NULL, to ignore the metabrowser completly. It is the subset of all_exp which are collections (the set of all experiments per organism), this will be fed to the metabrowser, while remaining all_exp are used in all other modules.

Value

RiboCrypt shiny app

Examples

run_variable <- 1 # Ignore check test limit
## Default run
# RiboCrypt_app()
## Plot on start
# RiboCrypt_app(browser_options = c(plot_on_start = "TRUE"))
## Init with an experiment and gene (you must of course have the experiment)

#RiboCrypt_app(validate.experiments = FALSE,
#       browser_options = c(plot_on_start = "TRUE",
#                           default_experiment = "all_merged-Homo_sapiens_2024_8",
#                           default_gene = "ATF4-ENSG00000128272"))
#RiboCrypt_app(validate.experiments = FALSE, all_exp = all_exp,
#browser_options = c(plot_on_start = "TRUE",
#                    default_experiment = "human_all_merged_l50",
#                    default_gene = "RPL12-ENSG00000197958",
#                    default_isoform = "ENST00000361436",
#                    default_view_mode = "genomic"))
#RiboCrypt_app(validate.experiments = FALSE,
#       browser_options = c(plot_on_start = "TRUE",
#                           default_experiment = "all_merged-Saccharomyces_cerevisiae",
#                           default_gene = "EFM5-YGR001",
#                           default_view_mode = "genomic"))

---