| Title: | Retrieving Information of Proteins from Uniprot |
| Version: | 2.5.0 |
| Author: | Mohamed Soudy [aut, cre], Ali Mostafa [aut] |
| Maintainer: | Mohamed Soudy <MohmedSoudy2009@gmail.com> |
| Description: | Connect to Uniprot https://www.uniprot.org/ to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <doi:10.1016/j.jprot.2019.103613>. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| Imports: | utils , grDevices , stats , grid , graphics , httr , plyr , dplyr , scales , magrittr , magick , data.tree , ggplot2 , tidyverse , gridExtra , ggpubr , curl, networkD3, stringr , qdapRegex , htmlwidgets , alakazam, gprofiler2, progress, ggsci |
| URL: | https://github.com/Proteomicslab57357/UniprotR |
| BugReports: | https://github.com/Proteomicslab57357/UniprotR/issues |
| NeedsCompilation: | no |
| Packaged: | 2025-06-15 10:26:54 UTC; mohamed.soudy |
| Repository: | CRAN |
| Date/Publication: | 2025-06-15 10:50:02 UTC |
Connect and parse UniProt information.
Description
This Function is used to plot Genes Tree in the data of the accession/s.
Usage
ConstructGenesTree(ProteinDataObject,directorypath = NULL)
Arguments
ProteinDataObject |
input a Dataframe returned from GetNamesTaxa function |
directorypath |
path to save txt file containig results returened by the function. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot location's Tree in the data of the accession/s in the chromosomes.
Usage
ConstructLocTree(ProteinDataObject,directorypath = NULL)
Arguments
ProteinDataObject |
input a Dataframe returned from GetNamesTaxa function |
directorypath |
path to save txt file containig results returened by the function. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt database identifiers information.
Description
The function is work to convert the UniProtKB AC/ID to any database identifiers available by the UniProtKB. For more information about available database identifiers see https://www.uniprot.org/help/id_mapping. see https://raw.githubusercontent.com/MohmedSoudy/UniprotR/master/uniprot_ids.csv
Usage
ConvertID(ProteinAccList,ID_from="UniProtKB_AC-ID",ID_to=NULL,taxId=NULL,path=NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
ID_from |
string of database identifier abbreviation, from which the Accession/ID will be converted |
ID_to |
string of database identifier abbreviation, to which the Accession/ID will be converted. default is all database identifier available in UniProtKB |
taxId |
string Needed when the ID_to is 'UniProtKB' that could be '9606' for human. |
path |
path to save excel file containig results returened by the function. |
Value
DataFrame where column one contains the Accession/ID before conversion and other columns contains the Accession/ID after conversion
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information
Description
This function is used for Enrichment analysis of biological process of given list of genes or proteins
Usage
Enrichment.BP(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL,top=10)
Arguments
Accs |
Vector of UniProt Accession/s or genes |
OS |
organism name Example: human - 'hsapiens', mouse - 'mmusculus' |
p_value |
custom p-value threshold for significance, default = 0.05 |
directorypath |
Path to save output plot |
top |
Top N terms to be visualized |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information
Description
This function is used for Enrichment analysis of cellular component of given list of genes or proteins
Usage
Enrichment.CC(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL,top=10)
Arguments
Accs |
Vector of UniProt Accession/s or genes |
OS |
organism name Example: human - 'hsapiens', mouse - 'mmusculus' |
p_value |
custom p-value threshold for significance, default = 0.05 |
directorypath |
Path to save output plot |
top |
Top N terms to be visualized |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information
Description
This function is used for Enrichment analysis of given list of genes or proteins from KEGG database
Usage
Enrichment.KEGG(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL,top=10)
Arguments
Accs |
Vector of UniProt Accession/s or genes |
OS |
organism name Example: human - 'hsapiens', mouse - 'mmusculus' |
p_value |
custom p-value threshold for significance, default = 0.05 |
directorypath |
Path to save output plot |
top |
Top N terms to be visualized |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information
Description
This function is used for Enrichment analysis of Molecular function of given list of genes or proteins
Usage
Enrichment.MF(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL,top=10)
Arguments
Accs |
Vector of UniProt Accession/s or genes |
OS |
organism name Example: human - 'hsapiens', mouse - 'mmusculus' |
p_value |
custom p-value threshold for significance, default = 0.05 |
directorypath |
Path to save output plot |
top |
Top N terms to be visualized |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information
Description
This function is used for Enrichment analysis of given list of genes or proteins from REACTOME
Usage
Enrichment.REAC(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL,top=10)
Arguments
Accs |
Vector of UniProt Accession/s or genes |
OS |
organism name Example: human - 'hsapiens', mouse - 'mmusculus' |
p_value |
custom p-value threshold for significance, default = 0.05 |
directorypath |
Path to save output plot |
top |
Top N terms to be visualized |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to get Sequence information of accession/s from Uniprot as a Fasta file.
Usage
GETSeqFastaUniprot(Accessions,FilePath = NULL, FileName = NULL)
Arguments
Accessions |
Vector of UniProt Accession/s |
FilePath |
path of directory to save the output fasta. |
FileName |
Name of the fasta file. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to get diseases associated with proteins.
Usage
Get.diseases(Pathology_object , directorypath = NULL)
Arguments
Pathology_object |
Dataframe retrieved from UniprotR Function "GetPathology_Biotech" |
directorypath |
path to save Output file |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This function can be used to get a list of UniProt Accession/s from a csv file.
Usage
GetAccessionList(DataObjPath)
Arguments
DataObjPath |
input path of excel file |
Value
a vector of UniProt Accession/s
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt Expression information.
Description
The function is work to retrieve Expression data from UniProt for a list of proteins accessions.For more information about what included in the Expression data see https://www.uniprot.org/help/return_fields.
Usage
GetExpression(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt Family Domains information.
Description
The function is work to retrieve Family Domains data from UniProt for a list of proteins accessions.For more information about what included in the Family Domains data see https://www.uniprot.org/help/return_fields.
Usage
GetFamily_Domains(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt General Information.
Description
The function is work to retrieve General Information data from UniProt for a list of proteins accessions.For more information about what included in the General Information data see https://www.uniprot.org/help/return_fields.
Usage
GetGeneral_Information(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the General Information of protein from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetGeneral_Information("O14520")
Connect and parse UniProt Miscellaneous information.
Description
The function is work to retrieve Miscellaneous data from UniProt for a list of proteins accessions.For more information about what included in the Miscellaneous data see https://www.uniprot.org/help/return_fields.
Usage
GetMiscellaneous(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetMiscellaneous("O14520")
Connect and parse UniProt Names Taxa information.
Description
The function is work to retrieve Names Taxa data from UniProt for a list of proteins accessions. For more information about what included in the NamesTaxa data see https://www.uniprot.org/help/return_fields.
Usage
GetNamesTaxa(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the information of protein name & taxonomy from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetNamesTaxa("O14520")
Connect and parse UniProt PTM_Processsing information.
Description
The function is work to retrieve PTM_Processsing data from UniProt for a list of proteins accessions. For more information about what included in the PTM_Processsing data see https://www.uniprot.org/help/return_fields.
Usage
GetPTM_Processing(ProteinAccList, directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function |
Value
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetPTM_Processing("O14520" )
Connect and parse UniProt Pathology_Biotech information.
Description
The function is work to retrieve Pathology_Biotech data from UniProt for a list of proteins accessions.For more information about what included in the Pathology_Biotech data see https://www.uniprot.org/help/return_fields.
Usage
GetPathology_Biotech(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetPathology_Biotech("O14520")
Connect and parse UniProt information.
Description
The function is work to retrieve user-defined information data from UniProt for a list of proteins accessions For more information see https://www.uniprot.org/help/uniprotkb_column_names
Usage
GetProteinAnnontate(ProteinAccList , columns)
Arguments
ProteinAccList |
a vector of UniProt Accession/s |
columns |
a vector of UniProtKB column names |
Value
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetProteinInteractions("O14520")
Connect and parse UniProt Protein Function information.
Description
The function is work to retrieve Protein Function data from UniProt for a list of proteins accessions.For more information about what included in the Protein Function data see https://www.uniprot.org/help/return_fields.
Usage
GetProteinFunction(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the information of protein function roles from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetProteinFunction("O14520")
Connect and parse UniProt proteins gene ontology information.
Description
The function is work to retrieve proteins gene ontology data from UniProt for a list of proteins accessions.For more information about what included in the proteins gene ontology data see https://www.uniprot.org/help/return_fields.
Usage
GetProteinGOInfo(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the information of Gene ontology of protein from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetProteinGOInfo("O14520")
Connect and parse UniProt protein Interactions information.
Description
The function is work to retrieve protein Interactions data from UniProt for a list of proteins accessions.For more information about what included in the protein Interactions data see https://www.uniprot.org/help/return_fields.
Usage
GetProteinInteractions(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the information of protein Interactions from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetProteinInteractions("ProteinAccession")
Connect and DOWNLOAD Proteome info.
Description
The function is work to retrieve proteome information in FASTA format based on proteome id.
Usage
GetProteomeFasta(ProteomeID , directorypath = NULL)
Arguments
ProteomeID |
Proteome ID from UniProt |
directorypath |
path to save FASTA file containig results returened by the function. |
Note
The function Download fasta format of proteome.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and DOWNLOAD Proteome info.
Description
The function is work to retrieve proteome information based on proteome id.
Usage
GetProteomeInfo(ProteomeID , directorypath = NULL)
Arguments
ProteomeID |
Proteome ID from UniProt |
directorypath |
path to save CSV file containig results returened by the function. |
Note
The function Download csv Info of proteome.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt Publication about a protein information.
Description
The function is work to retrieve Publication data from UniProt for a list of proteins accessions. For more information about what included in the Publication data see https://www.uniprot.org/help/return_fields.
Usage
GetPublication(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the Publication of protein from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt Sequences information.
Description
The function is work to retrieve Sequence's Length data from Uniparc for a list of proteins accessions. This function was added to overcome the NAs returned when Uniprot database deleted the protein from the database
Usage
GetSeqLength(ProteinAccList, directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function |
Value
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetSeqLength("O14520")
Connect and parse UniProt Sequences information.
Description
The function is work to retrieve protein's Sequence data from Uniparc for a list of proteins accessions. This function was added to handle isoformes
Usage
GetSequenceIso(ProteinAccList, directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function |
Value
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetSequenceIso("O14520")
Connect and parse UniProt Sequences information.
Description
The function is work to retrieve Sequences data from UniProt for a list of proteins accessions. For more information about what included in the Sequences data see https://www.uniprot.org/help/return_fields.
Usage
GetSequences(ProteinAccList, directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function |
Value
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
Obj <- GetSequences("O14520")
Connect and parse UniProt protein Structure information.
Description
The function is work to retrieve Structral data from UniProt for a list of proteins accessions. For more information about what included in the structral data see https://www.uniprot.org/help/return_fields.
Usage
GetStructureInfo(ProteinAccList, directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s. |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the Structural information of protein from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Connect and parse UniProt protein Subcellular location information.
Description
The function is work to retrieve protein Subcellular location data from UniProt for a list of proteins accessions. For more information about what included in the protein Subcellular location data see https://www.uniprot.org/help/return_fields.
Usage
GetSubcellular_location(ProteinAccList, directorypath = NULL)
Arguments
ProteinAccList |
Vector of UniProt Accession/s. |
directorypath |
path to save excel file containig results returened by the function. |
Value
DataFrame where rows names are the accession and columns contains the information about Subcellular location of protein from the UniProt
Note
The function also, Creates a csv file with the retrieved information.
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
The function is work to retrieving GetpdbStructure and download it to user directory.
Usage
GetpdbStructure(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
input a vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse stringdb information.
Description
This function is connecting to stringdb and retrieve all possible interactions for the searched protein/s.
Usage
GetproteinNetwork(ProteinAccList , directorypath = NULL)
GetproteinNetwork(ProteinAccList , directorypath = NULL)
Arguments
ProteinAccList |
input a vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse stringdb information.
Description
This function is connecting to stringdb and retrieve PPI between input list
Usage
GetproteinNetwork_all(ProteinAccList , directorypath = NULL, SpeciesID = 9606)
GetproteinNetwork_all(ProteinAccList , directorypath = NULL,SpeciesID = 9606)
Arguments
ProteinAccList |
input a vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
SpeciesID |
Taxonomic id of accession's species ex. homo sapines 9606 |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to parse data retrieved from UniprotR Function "GetProteinGOInfo".
Usage
Goparse(GOObj , index = 3)
Arguments
GOObj |
Dataframe. |
index |
idex of Go term in GoObj |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Handle bad requests This Function is used to handle possible errors when trying to get url response.
Description
Handle bad requests This Function is used to handle possible errors when trying to get url response.
Usage
HandleBadRequests(RequestCode)
Arguments
RequestCode |
Response returned from url |
Value
None
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Examples
HandleBadRequests(400)
Connect and parse UniProt information
Description
This function is used for Enrichment analysis of given list of genes or proteins
Usage
Pathway.Enr(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL,top=10)
Arguments
Accs |
Vector of UniProt Accession/s or genes |
OS |
organism Example: human - 'hsapiens' for more info https://biit.cs.ut.ee/gprofiler/page/organism-list |
p_value |
custom p-value threshold for significance, default = 0.05 |
directorypath |
Path to save output plot |
top |
Top N terms to be visualized |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot Molecular function of proteins.
Usage
Plot.GOMolecular(GOObj, Top = 10, directorypath = NULL)
Arguments
GOObj |
Dataframe returned from UniprotR Function "GetProteinGOInfo" |
Top |
Number of molecular functions to be visualized |
directorypath |
path to save Output plot. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot subcellular localization of proteins.
Usage
Plot.GOSubCellular(GOObj, Top = 10, directorypath = NULL)
Arguments
GOObj |
Dataframe returned from UniprotR Function "GetProteinGOInfo" |
Top |
Number of molecular functions to be visualized |
directorypath |
path to save Output plot. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot proteins acidity retrieved from "GetSequences" Function.
Usage
PlotAcidity(SeqDataObjPath , directorypath = NULL)
Arguments
SeqDataObjPath |
Dataframe retrieved from UniprotR Function "GetSequences" |
directorypath |
path to save Output plot. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot proteins charge retrieved from "GetSequences" Function.
Usage
PlotCharge(SeqDataObjPath , directorypath = NULL)
Arguments
SeqDataObjPath |
Dataframe retrieved from UniprotR Function "GetSequences" |
directorypath |
path to save Output plot. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot location's frequency in the data of the accession/s in the chromosomes.
Usage
PlotChromosomeInfo(ProteinDataObject,directorypath = NULL)
Arguments
ProteinDataObject |
input a Dataframe returned from GetNamesTaxa function |
directorypath |
path to save files returened by the function. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot the retrieved Gene Ontology from function 'GetProteinGOInfo'.
Usage
PlotGOAll(GOObj, Top = 10, directorypath = NULL, width = width, height = height)
Arguments
GOObj |
Dataframe returned from UniprotR Function "GetProteinGOInfo" |
Top |
Number of molecular functions to be visualized |
directorypath |
path to save Output plot. |
width |
width of the generated plot |
height |
height of the generated plot |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot Biological process of proteins.
Usage
PlotGOBiological(GOObj, Top = 10, directorypath = NULL)
Arguments
GOObj |
Dataframe returned from UniprotR Function "GetProteinGOInfo" |
Top |
Number of molecular functions to be visualized |
directorypath |
path to save Output plot. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to cluster proteins based on primary genes retrieved from "GetNamesTaxa" Function.
Usage
PlotGenesNetwork(ProteinDataObject , directorypath = NULL)
Arguments
ProteinDataObject |
Dataframe retrieved from UniprotR Function "GetNamesTaxa" |
directorypath |
path to save Output plot. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot data retrieved from UniprotR Function "GetProteinGOInfo".
Usage
PlotGoInfo(GOObj , directorypath = NULL)
Arguments
GOObj |
Dataframe retrieved from UniprotR Function "GetProteinGOInfo". |
directorypath |
path to save excel file containig results returened by the function ( default = NA ). |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot data retrieved from UniprotR Function "GetProteinGOInfo".
Usage
PlotGoterms(GOObj , directorypath = NULL)
Arguments
GOObj |
Dataframe. |
directorypath |
path to save plot returned by function ( default = NA ). |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot proteins gravy index retrieved from "GetSequences" Function.
Usage
PlotGravy(SeqDataObjPath , directorypath = NULL)
Arguments
SeqDataObjPath |
Dataframe retrieved from UniprotR Function "GetSequences" |
directorypath |
path to save Output plot. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This function can be used to get a list of UniProt Accession/s from a csv file.
Usage
PlotPhysicochemical(SeqDataObjPath , directorypath = NULL)
Arguments
SeqDataObjPath |
Dataframe returned from GetSequence function. |
directorypath |
Path to save Physcochemical properties plot. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot biological process data retrieved from UniprotR Function "GetProteinGOInfo".
Usage
PlotProteinGO_bio(GO_df , dir_path = NA)
Arguments
GO_df |
Dataframe. |
dir_path |
path to save files returened by the function ( default = NA ). |
Note
if no dir_path was given ( default = NA ) the function will only view the plot and will not save it
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot cellular components data retrieved from UniprotR Function "GetProteinGOInfo".
Usage
PlotProteinGO_cel(GO_df , dir_path = NA)
Arguments
GO_df |
Dataframe. |
dir_path |
path to save files returened by the function ( default = NA ). |
Note
if no dir_path was given ( default = NA ) the function will only view the plot and Will not save it
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot molecular functions data retrieved from UniprotR Function "GetProteinGOInfo".
Usage
PlotProteinGO_molc(GO_df , dir_path = NA)
Arguments
GO_df |
Dataframe. |
dir_path |
path to save files returened by the function ( default = NA ). |
Note
if no dir_path was given ( default = NA ) the function will only view the plot and will not save it
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot different taxas found of the accessions.
Usage
PlotProteinTaxa(ProteinDataObject , directorypath = NULL)
Arguments
ProteinDataObject |
input a Dataframe of proteins as rownames. |
directorypath |
path to save files returened by the function. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot protein status in the data of the accession/s.
Usage
PlotproteinExist(ProteinDataObject,directorypath = NULL)
Arguments
ProteinDataObject |
input a Dataframe returned from GetMiscellaneous function |
directorypath |
path to save files returened by the function. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot protein status in the data of the accession/s.
Usage
PlotproteinStatus (ProteinDataObject,directorypath = NULL)
Arguments
ProteinDataObject |
input a Dataframe returned from GetMiscellaneous function |
directorypath |
path to save files returened by the function. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to check validty of input accessions the data of the accession/s.
Usage
ProcessAcc(Accessions)
Arguments
Accessions |
acession list returened from GetAccession function |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg
Connect and parse UniProt information.
Description
This Function is used to plot Gene ontolgy summary in the data of the accession/s.
Usage
plotGoannotation(ProteinDataObject,directorypath = NULL)
Arguments
ProteinDataObject |
input a Dataframe returned from GetProteinGOInfo function |
directorypath |
path to save files returened by the function. |
Author(s)
Mohmed Soudy Mohamed.soudy@57357.com and Ali Mostafa ali.mo.anwar@std.agr.cu.edu.eg