Type:	Package
Title:	Visualizing the Elements Within Bio-Sequences
Version:	1.0.4
Maintainer:	Shiqi Zhao <zhaosq89@163.com>
Description:	Visualizing the types and distribution of elements within bio-sequences. At the same time, We have developed a geom layer, geom_rrect(), that can generate rounded rectangles. No external references are used in the development of this package.
Encoding:	UTF-8
License:	Artistic-2.0
Language:	en-US
RoxygenNote:	7.2.3
Repository:	CRAN
Imports:	dplyr, ggplot2, httr, RColorBrewer, seqinr, stringr, tidyr, magrittr, ggtree, treeio, ggh4x, shiny
NeedsCompilation:	no
Packaged:	2025-08-22 07:50:21 UTC; zhaoshiqi
Author:	Shiqi Zhao [aut, cre, cph]
Date/Publication:	2025-08-22 08:10:02 UTC

ProtParam_calc

Description

Extract the information of protein sequence

Usage

ProtParam_calc(input_file)

Arguments

Value

data.frame

Author(s)

Shiqi Zhao

BioVizSeq shiny app start function.

Description

BioVizSeq shiny app start function.

Usage

biovizseq()

Value

Shinyapp: BioVizSeq shiny app.

Author(s)

Shiqi Zhao

Examples

# 1. Library BioVizSeq package
library(BioVizSeq)

cdd_plot

Description

Visualization of domain in CDD file

Usage

cdd_plot(
  cdd_file,
  fasta_file,
  the_order = NULL,
  domain_select = NULL,
  shape = "RoundRect",
  r = 0.3,
  legend_size = 15,
  domain_color = NULL
)

Arguments

Value

p

Author(s)

Shiqi Zhao

Examples

hitdata_path <- system.file("extdata", "hitdata.txt", package = "BioVizSeq")
fa_path <- system.file("extdata", "idpep.fa", package = "BioVizSeq")
cdd_plot(hitdata_path, fa_path)

order_path <- system.file("extdata", "order.csv", package = "BioVizSeq")
cdd_plot(hitdata_path, fa_path, the_order = order_path)

cdd_to_loc

Description

Extract the location information of domain from cdd file

Usage

cdd_to_loc(cdd_file)

Arguments

Value

data.frame

Author(s)

Shiqi Zhao

Examples

hitdata_path <- system.file("extdata", "hitdata.txt", package = "BioVizSeq")
cdd_file <- readLines(hitdata_path)
domain_loc <- cdd_to_loc(cdd_file)

combi_p

Description

Get ggplot2 files to facilitate free combination in patchwork

Usage

combi_p(
  tree_path,
  gff_path = NULL,
  meme_path = NULL,
  pfam_path = NULL,
  cdd_path = NULL,
  fa_path = NULL,
  smart_path = FALSE,
  plantcare_path = NULL,
  promoter_length = NULL,
  renamefile = NULL,
  groupfile = NULL,
  shape = "RoundRect",
  r = 0.3,
  legend_size = 6
)

Arguments

Value

list

Author(s)

Shiqi Zhao

Examples

tree_path <- system.file("extdata", "idpep.nwk", package = "BioVizSeq")
plot_file <- combi_p(tree_path)

combi_p2

Description

Get ggplot2 files to facilitate free combination in patchwork

Usage

combi_p2(
  order_path,
  gff_path = NULL,
  meme_path = NULL,
  pfam_path = NULL,
  cdd_path = NULL,
  fa_path = NULL,
  smart_path = FALSE,
  plantcare_path = NULL,
  promoter_length = NULL,
  renamefile = NULL,
  shape = "RoundRect",
  r = 0.3,
  legend_size = 6
)

Arguments

Value

list

Author(s)

Shiqi Zhao

Examples

order_path <- system.file("extdata", "order.csv", package = "BioVizSeq")
gff_path <- system.file("extdata", "idpro.gff3", package = "BioVizSeq")
plot_file <- combi_p2(order_path, gff_path = gff_path)

fastaleng

Description

Statistical sequence length

Usage

fastaleng(fasta_file)

Arguments

Value

data.frame

Author(s)

Shiqi Zhao

Examples

fasta_path <- system.file("extdata", "idpep.fa", package = "BioVizSeq") 
fastaleng(fasta_path)

geom_rrect

Description

Rounded rectangle

Usage

geom_rrect(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  r = 0.2,
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

Details

draws rounded rectangle by using the locations of the four corners (xmin, xmax, ymin and ymax) like geom_rect().

Value

ggplot object

Aesthetics

geom_rrect() understands the following aesthetics (required aesthetics are in bold):

• xmin

• xmax

• ymin

• ymax

• alpha

• colour

• fill

• group

• linetype

Learn more about setting these aesthetics in vignette("ggplot2-specs").

Author(s)

Shiqi Zhao

Examples

library(ggplot2)
df <- data.frame(
 xmin = c(1, 2, 3),
 xmax = c(2, 3, 4),
 ymin = c(1, 2, 3),
 ymax = c(2, 3, 4),
 category = c("A", "B", "C")
 )
 
 p <- ggplot(df) +
   geom_rrect(aes(xmin = xmin, xmax = xmax, 
              ymin = ymin, ymax = ymax, fill = category), 
             r = 0.4, linewidth = 1, colour = "black") 
 
 print(p)

gff_plot

Description

Visualization of element in gff or gtf file

Usage

gff_plot(
  gff_file,
  the_order = NULL,
  shape = "Rect",
  r = 0.3,
  legend_size = 15,
  element_color = NULL
)

Arguments

Value

p

Author(s)

Shiqi Zhao

Examples

gff_path <- system.file("extdata", "test.gff", package = "BioVizSeq")
gff_plot(gff_path)

gff_statistics

Description

Extract the information of element from gff or gtf file

Usage

gff_statistics(gff_data, mRNA_ID = NULL)

Arguments

Value

data.frame

Author(s)

Shiqi Zhao

Examples

gff_path <- system.file("extdata", "idpro.gff3", package = "BioVizSeq")
gff_data <- read.table(gff_path, header = FALSE, sep = '\t')
gff_statistics_data <- gff_statistics(gff_data)

gff_to_loc

Description

Extract the location information of element from gff or gtf file

Usage

gff_to_loc(gff_data, mRNA_ID = NULL)

Arguments

Value

list

Author(s)

Shiqi Zhao

Examples

gff_path <- system.file("extdata", "test.gff", package = "BioVizSeq")
gff_data <- read.table(gff_path, header = FALSE, sep = '\t')
gff_loc <- gff_to_loc(gff_data)

ID_path <- system.file("extdata", "ID_select.csv", package = "BioVizSeq")
mRNA_ID <- readLines(ID_path) 
gff_loc <- gff_to_loc(gff_data, mRNA_ID=mRNA_ID)

Global Variables Declaration

Description

Global Variables

Details

This block declares global variables to avoid R CMD check warnings.

meme_plot

Description

Visualization of motif in meme file or mast file

Usage

meme_plot(
  meme_file,
  the_order = NULL,
  motif_select = NULL,
  shape = "RoundRect",
  show_motif_id = FALSE,
  r = 0.3,
  legend_size = 15,
  motif_color = NULL
)

Arguments

Value

p

Author(s)

Shiqi Zhao

Examples

mast_path <- system.file("extdata", "mast.xml", package = "BioVizSeq")
meme_plot(mast_path)

meme_plot(mast_path, motif_select="1", show_motif_id = TRUE)

order_path <- system.file("extdata", "order.csv", package = "BioVizSeq")
meme_plot(mast_path, the_order=order_path, motif_select="1")

meme_seq

Description

Get motif sequence from meme file or mast file

Usage

meme_seq(meme_file)

Arguments

Value

data.frame

Author(s)

Shiqi Zhao

Examples

mast_path <- system.file("extdata", "mast.xml", package = "BioVizSeq")
mast_file <- readLines(mast_path)
motifseq<- meme_seq(mast_file)

meme_to_loc

Description

Extract the location information of motif from mast or meme file

Usage

meme_to_loc(motif_file)

Arguments

Value

list

Author(s)

Shiqi Zhao

Examples

mast_path <- system.file("extdata", "mast.xml", package = "BioVizSeq") 
mast_file <- readLines(mast_path)
motif_loc <- meme_to_loc(mast_file)

motif_plot

Description

Draws multiple rounded rectangle.

Usage

motif_plot(
  motif_loc,
  gene_length,
  the_order = NULL,
  motif_select = NULL,
  shape = "RoundRect",
  show_motif_id = FALSE,
  r = 0.3,
  legend_size = 15,
  motif_color = NULL
)

Arguments

Details

motif_plot() draws multiple rounded rectangle to represent the above elements of biosequences, but not limited to biosequences

Value

p

Author(s)

Shiqi Zhao

Examples

df <- data.frame(
 ID = rep(c("geneA", "geneB", "geneC"), each = 3),
 motif = rep(c("1", "2", "3"), times = 3),
 start = c(1, 3, 6, 1, 6, 10, 10, 7, 17),
 end = c(3, 5, 11, 3, 8, 15, 12, 9, 22)
 )
 
 length_data <- data.frame(
 ID = c("geneA", "geneB", "geneC"),
 length = c(15, 27, 30)
 )
 
 order_data <- c("geneB", "geneA", "geneC")
 
 motif_plot(df, length_data)
 motif_plot(df, length_data, the_order = order_data)

pfam_plot

Description

Visualization of domain in pfam result file

Usage

pfam_plot(
  pfam_file,
  the_order = NULL,
  domain_select = NULL,
  shape = "RoundRect",
  r = 0.3,
  legend_size = 15,
  domain_color = NULL
)

Arguments

Value

p

Author(s)

Shiqi Zhao

Examples

pfam_path <- system.file("extdata", "iprscan.tsv", package = "BioVizSeq")
order_path <- system.file("extdata", "order.csv", package = "BioVizSeq")
pfam_plot(pfam_path)
pfam_plot(pfam_path, the_order=order_path)

pfam_to_loc

Description

Extract the location information of domain from pfam result

Usage

pfam_to_loc(pfam_data)

Arguments

Value

list

Author(s)

Shiqi Zhao

Examples

pfam_path <- system.file("extdata", "iprscan.tsv", package = "BioVizSeq")
pfam_file <- read.table(pfam_path, sep='\t', header = FALSE)
motif_loc <- pfam_to_loc(pfam_file)

plantcare_classify

Description

Classify the functions of cis element from Plantcare

Usage

plantcare_classify(plantcare_file)

Arguments

Value

data.frame

Author(s)

Shiqi Zhao

Examples

plantcare_path <- system.file("extdata", "plantCARE_output.tab", package = "BioVizSeq") 
plantcare_file <- read.table(plantcare_path, header = FALSE, sep = '\t', quote="")
plantcare_data <- plantcare_classify(plantcare_file)

plantcare_plot

Description

Visualization of cis-element in plantcare result file

Usage

plantcare_plot(
  plantcare_file,
  promoter_length = 2000,
  the_order = NULL,
  shape = "Rect",
  r = 6,
  legend_size = 15,
  element_color = NULL
)

Arguments

Value

p

Author(s)

Shiqi Zhao

Examples

plantcare_path <- system.file("extdata", "plantCARE_output.tab", package = "BioVizSeq") 
plantcare_plot(plantcare_path, promoter_length = 2000)

plantcare_plot1

Description

Heatmap of the number of cis-element in plantcare result file

Usage

plantcare_plot1(plantcare_file, the_order = NULL)

Arguments

Value

p

Author(s)

Shiqi Zhao

Examples

plantcare_path <- system.file("extdata", "plantCARE_output.tab", package = "BioVizSeq") 
plantcare_plot1(plantcare_path)

plantcare_plot2

Description

Bar plot1 of the number of cis-element in plantcare result file

Usage

plantcare_plot2(plantcare_file, the_order = NULL)

Arguments

Value

p

Author(s)

Shiqi Zhao

Examples

plantcare_path <- system.file("extdata", "plantCARE_output.tab", package = "BioVizSeq") 
plantcare_plot2(plantcare_path)

plantcare_plot3

Description

Bar plot2 of the number of cis-element in plantcare result file

Usage

plantcare_plot3(plantcare_file, the_order = NULL)

Arguments

Value

p

Author(s)

Shiqi Zhao

Examples

plantcare_path <- system.file("extdata", "plantCARE_output.tab", package = "BioVizSeq") 
plantcare_plot3(plantcare_path)

plantcare_statistic1

Description

Count the number of cis element from Plantcare for heatmap

Usage

plantcare_statistic1(plantcare_data)

Arguments

Value

data.frame

Author(s)

Shiqi Zhao

Examples

plantcare_path <- system.file("extdata", "plantCARE_output.tab", package = "BioVizSeq") 
plantcare_file <- read.table(plantcare_path, header = FALSE, sep = '\t', quote="")
plantcare_data <- plantcare_classify(plantcare_file)
statistic_data1 <- plantcare_statistic1(plantcare_data)

plantcare_statistic2

Description

Count the number of cis element from Plantcare for Bar chart

Usage

plantcare_statistic2(plantcare_data)

Arguments

Value

data.frame

Author(s)

Shiqi Zhao

Examples

plantcare_path <- system.file("extdata", "plantCARE_output.tab", package = "BioVizSeq") 
plantcare_file <- read.table(plantcare_path, header = FALSE, sep = '\t', quote="")
plantcare_data <- plantcare_classify(plantcare_file)
statistic_data2 <- plantcare_statistic2(plantcare_data)

plantcare_to_loc

Description

Extract the location information of cis-element from Plantcare

Usage

plantcare_to_loc(plantcare_data)

Arguments

Value

data.frame

Author(s)

Shiqi Zhao

Examples

plantcare_path <- system.file("extdata", "plantCARE_output.tab", package = "BioVizSeq") 
plantcare_file <- read.table(plantcare_path, header = FALSE, sep = '\t', quote="")
plantcare_data <- plantcare_classify(plantcare_file)
plantcare_loc <- plantcare_to_loc(plantcare_data)

smart_plot

Description

Visualization of domain in SMART result file

Usage

smart_plot(
  fasta_file,
  the_order = NULL,
  domain_select = NULL,
  shape = "RoundRect",
  r = 0.3,
  legend_size = 15,
  domain_color = NULL
)

Arguments

Value

p

Author(s)

Shiqi Zhao

smart_to_loc

Description

Extract the location information of domain from SMART result

Usage

smart_to_loc(input_file, do_pfam = TRUE)

Arguments

Value

list

Author(s)

Shiqi Zhao

upload_fa_to_plantcare

Description

Upload the promoter file to Plantcare database

Usage

upload_fa_to_plantcare(fasta_file, email)

Arguments

Details

Due to the file size limitation of plantcare on fasta, upload_fa_to_plantcare() first splits fasta file. Then uploads the splited fasta files to the plantcare database, and automatically returns the results to the email provided by the user.

upload_fa_to_plantcare("the path/test.fasta", "your e-mail address")

Value

plantcare_result

Author(s)

Shiqi Zhao