| Title: | Retrieving Information of Proteins from Uniprot |
|---|---|
| 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 <https://www.sciencedirect.com/science/article/pii/S1874391919303859>. |
| Authors: | Mohamed Soudy [aut, cre], Ali Mostafa [aut] |
| Maintainer: | Mohamed Soudy <[email protected]> |
| License: | GPL-3 |
| Version: | 2.2.1 |
| Built: | 2025-02-12 04:43:22 UTC |
| Source: | https://github.com/proteomicslab57357/uniprotr |
This Function is used to plot Genes Tree in the data of the accession/s.
ConstructGenesTree(ProteinDataObject,directorypath = NULL)ConstructGenesTree(ProteinDataObject,directorypath = NULL)
ProteinDataObject |
input a Dataframe returned from GetNamesTaxa function |
directorypath |
path to save txt file containig results returened by the function. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot location's Tree in the data of the accession/s in the chromosomes.
ConstructLocTree(ProteinDataObject,directorypath = NULL)ConstructLocTree(ProteinDataObject,directorypath = NULL)
ProteinDataObject |
input a Dataframe returned from GetNamesTaxa function |
directorypath |
path to save txt file containig results returened by the function. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
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/api_idmapping.
ConvertID(ProteinAccList , ID_from = "ACC+ID" , ID_to = NULL , directorypath = NULL)ConvertID(ProteinAccList , ID_from = "ACC+ID" , ID_to = NULL , directorypath = NULL)
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 |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where column one contains the Accession/ID before conversion and other columns contains the Accession/ID after conversion
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function is used for Enrichment analysis of biological process of given list of genes or proteins
Enrichment.BP(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)Enrichment.BP(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)
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 |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function is used for Enrichment analysis of cellular component of given list of genes or proteins
Enrichment.CC(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)Enrichment.CC(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)
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 |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function is used for Enrichment analysis of given list of genes or proteins from KEGG database
Enrichment.KEGG(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)Enrichment.KEGG(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)
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 |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function is used for Enrichment analysis of Molecular function of given list of genes or proteins
Enrichment.MF(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)Enrichment.MF(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)
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 |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function is used for Enrichment analysis of given list of genes or proteins from REACTOME
Enrichment.REAC(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)Enrichment.REAC(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)
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 |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to get diseases associated with proteins.
Get.diseases(Pathology_object , directorypath = NULL)Get.diseases(Pathology_object , directorypath = NULL)
Pathology_object |
Dataframe retrieved from UniprotR Function "GetPathology_Biotech" |
directorypath |
path to save Output file |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function can be used to get a list of UniProt Accession/s from a csv file.
GetAccessionList(DataObjPath)GetAccessionList(DataObjPath)
DataObjPath |
input path of excel file |
a vector of UniProt Accession/s
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
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.
GetExpression(ProteinAccList , directorypath = NULL)GetExpression(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
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.
GetFamily_Domains(ProteinAccList , directorypath = NULL)GetFamily_Domains(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
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.
GetGeneral_Information(ProteinAccList , directorypath = NULL)GetGeneral_Information(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the General Information of protein from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetGeneral_Information("O14520")Obj <- GetGeneral_Information("O14520")
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.
GetMiscellaneous(ProteinAccList , directorypath = NULL)GetMiscellaneous(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetMiscellaneous("O14520")Obj <- GetMiscellaneous("O14520")
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.
GetNamesTaxa(ProteinAccList , directorypath = NULL)GetNamesTaxa(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the information of protein name & taxonomy from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetNamesTaxa("O14520")Obj <- GetNamesTaxa("O14520")
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.
GetPathology_Biotech(ProteinAccList , directorypath = NULL)GetPathology_Biotech(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetPathology_Biotech("O14520")Obj <- GetPathology_Biotech("O14520")
The function is work to retrieving GetpdbStructure and download it to user directory.
GetpdbStructure(ProteinAccList , directorypath = NULL)GetpdbStructure(ProteinAccList , directorypath = NULL)
ProteinAccList |
input a vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
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
GetProteinAnnontate(ProteinAccList , columns)GetProteinAnnontate(ProteinAccList , columns)
ProteinAccList |
a vector of UniProt Accession/s |
columns |
a vector of UniProtKB column names |
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetProteinInteractions("O14520")Obj <- GetProteinInteractions("O14520")
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.
GetProteinFunction(ProteinAccList , directorypath = NULL)GetProteinFunction(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the information of protein function roles from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetProteinFunction("O14520")Obj <- GetProteinFunction("O14520")
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.
GetProteinGOInfo(ProteinAccList , directorypath = NULL)GetProteinGOInfo(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the information of Gene ontology of protein from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetProteinGOInfo("O14520")Obj <- GetProteinGOInfo("O14520")
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.
GetProteinInteractions(ProteinAccList , directorypath = NULL)GetProteinInteractions(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the information of protein Interactions from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetProteinInteractions("ProteinAccession")Obj <- GetProteinInteractions("ProteinAccession")
This function is connecting to stringdb and retrieve all possible interactions for the searched protein/s.
GetproteinNetwork(ProteinAccList , directorypath = NULL) GetproteinNetwork(ProteinAccList , directorypath = NULL)GetproteinNetwork(ProteinAccList , directorypath = NULL) GetproteinNetwork(ProteinAccList , directorypath = NULL)
ProteinAccList |
input a vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function is connecting to stringdb and retrieve PPI between input list
GetproteinNetwork_all(ProteinAccList , directorypath = NULL, SpeciesID = 9606) GetproteinNetwork_all(ProteinAccList , directorypath = NULL,SpeciesID = 9606)GetproteinNetwork_all(ProteinAccList , directorypath = NULL, SpeciesID = 9606) GetproteinNetwork_all(ProteinAccList , directorypath = NULL,SpeciesID = 9606)
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 |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
The function is work to retrieve proteome information in FASTA format based on proteome id.
GetProteomeFasta(ProteomeID , directorypath = NULL)GetProteomeFasta(ProteomeID , directorypath = NULL)
ProteomeID |
Proteome ID from UniProt |
directorypath |
path to save FASTA file containig results returened by the function. |
The function Download fasta format of proteome.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
The function is work to retrieve proteome information based on proteome id.
GetProteomeInfo(ProteomeID , directorypath = NULL)GetProteomeInfo(ProteomeID , directorypath = NULL)
ProteomeID |
Proteome ID from UniProt |
directorypath |
path to save CSV file containig results returened by the function. |
The function Download csv Info of proteome.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
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.
GetPTM_Processing(ProteinAccList, directorypath = NULL)GetPTM_Processing(ProteinAccList, directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function |
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetPTM_Processing("O14520" )Obj <- GetPTM_Processing("O14520" )
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.
GetPublication(ProteinAccList , directorypath = NULL)GetPublication(ProteinAccList , directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the Publication of protein from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to get Sequence information of accession/s from Uniprot as a Fasta file.
GETSeqFastaUniprot(Accessions,FilePath = NULL, FileName = NULL)GETSeqFastaUniprot(Accessions,FilePath = NULL, FileName = NULL)
Accessions |
Vector of UniProt Accession/s |
FilePath |
path of directory to save the output fasta. |
FileName |
Name of the fasta file. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
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
GetSeqLength(ProteinAccList, directorypath = NULL)GetSeqLength(ProteinAccList, directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function |
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetSeqLength("O14520")Obj <- GetSeqLength("O14520")
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
GetSequenceIso(ProteinAccList, directorypath = NULL)GetSequenceIso(ProteinAccList, directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function |
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetSequenceIso("O14520")Obj <- GetSequenceIso("O14520")
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.
GetSequences(ProteinAccList, directorypath = NULL)GetSequences(ProteinAccList, directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s |
directorypath |
path to save excel file containig results returened by the function |
DataFrame where rows names are the accession and columns contains the information retrieved from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Obj <- GetSequences("O14520")Obj <- GetSequences("O14520")
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.
GetStructureInfo(ProteinAccList, directorypath = NULL)GetStructureInfo(ProteinAccList, directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s. |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the Structural information of protein from the UniProt
The function also, Creates a csv file with the retrieved information.
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.
GetSubcellular_location(ProteinAccList, directorypath = NULL)GetSubcellular_location(ProteinAccList, directorypath = NULL)
ProteinAccList |
Vector of UniProt Accession/s. |
directorypath |
path to save excel file containig results returened by the function. |
DataFrame where rows names are the accession and columns contains the information about Subcellular location of protein from the UniProt
The function also, Creates a csv file with the retrieved information.
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to parse data retrieved from UniprotR Function "GetProteinGOInfo".
Goparse(GOObj , index = 3)Goparse(GOObj , index = 3)
GOObj |
Dataframe. |
index |
idex of Go term in GoObj |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
Handle bad requests This Function is used to handle possible errors when trying to get url response.
HandleBadRequests(RequestCode)HandleBadRequests(RequestCode)
RequestCode |
Response returned from url |
None
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
HandleBadRequests(400)HandleBadRequests(400)
This function is used for Enrichment analysis of given list of genes or proteins
Pathway.Enr(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)Pathway.Enr(Accs,OS="hsapiens",p_value=0.05,directorypath=NULL)
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 |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot Molecular function of proteins.
Plot.GOMolecular(GOObj, Top = 10, directorypath = NULL)Plot.GOMolecular(GOObj, Top = 10, directorypath = NULL)
GOObj |
Dataframe returned from UniprotR Function "GetProteinGOInfo" |
Top |
Number of molecular functions to be visualized |
directorypath |
path to save Output plot. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot subcellular localization of proteins.
Plot.GOSubCellular(GOObj, Top = 10, directorypath = NULL)Plot.GOSubCellular(GOObj, Top = 10, directorypath = NULL)
GOObj |
Dataframe returned from UniprotR Function "GetProteinGOInfo" |
Top |
Number of molecular functions to be visualized |
directorypath |
path to save Output plot. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot proteins acidity retrieved from "GetSequences" Function.
PlotAcidity(SeqDataObjPath , directorypath = NULL)PlotAcidity(SeqDataObjPath , directorypath = NULL)
SeqDataObjPath |
Dataframe retrieved from UniprotR Function "GetSequences" |
directorypath |
path to save Output plot. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot proteins charge retrieved from "GetSequences" Function.
PlotCharge(SeqDataObjPath , directorypath = NULL)PlotCharge(SeqDataObjPath , directorypath = NULL)
SeqDataObjPath |
Dataframe retrieved from UniprotR Function "GetSequences" |
directorypath |
path to save Output plot. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot location's frequency in the data of the accession/s in the chromosomes.
PlotChromosomeInfo(ProteinDataObject,directorypath = NULL)PlotChromosomeInfo(ProteinDataObject,directorypath = NULL)
ProteinDataObject |
input a Dataframe returned from GetNamesTaxa function |
directorypath |
path to save files returened by the function. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function is used to generate a combined plot for the enriched Gene Ontology terms
PlotEnrichedGO(Accs,OS="hsapiens",p_value=0.05,Path=NULL,theme="aaas",width=7,height=7)PlotEnrichedGO(Accs,OS="hsapiens",p_value=0.05,Path=NULL,theme="aaas",width=7,height=7)
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 |
Path |
Path to save output plot |
theme |
optional parameter to generate specific theme for journals ex: "aaas", "nature", "lancet", "jama" |
width |
width of the generated plot |
height |
height of the generated plot |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function is used to generate a combined plot for the enriched pathways from KEGG and REACTOME
PlotEnrichedPathways(Accs,OS="hsapiens",p_value=0.05,Path=NULL,theme="aaas",w=w,h=h)PlotEnrichedPathways(Accs,OS="hsapiens",p_value=0.05,Path=NULL,theme="aaas",w=w,h=h)
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 |
Path |
Path to save output plot |
theme |
optional parameter to generate specific theme for journals ex: "aaas", "nature", "lancet", "jama" |
w |
width of the generated plot |
h |
height of the generated plot |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to cluster proteins based on primary genes retrieved from "GetNamesTaxa" Function.
PlotGenesNetwork(ProteinDataObject , directorypath = NULL)PlotGenesNetwork(ProteinDataObject , directorypath = NULL)
ProteinDataObject |
Dataframe retrieved from UniprotR Function "GetNamesTaxa" |
directorypath |
path to save Output plot. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot the retrieved Gene Ontology from function 'GetProteinGOInfo'.
PlotGOAll(GOObj, Top = 10, directorypath = NULL, width = width, height = height)PlotGOAll(GOObj, Top = 10, directorypath = NULL, width = width, height = height)
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 |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot Biological process of proteins.
PlotGOBiological(GOObj, Top = 10, directorypath = NULL)PlotGOBiological(GOObj, Top = 10, directorypath = NULL)
GOObj |
Dataframe returned from UniprotR Function "GetProteinGOInfo" |
Top |
Number of molecular functions to be visualized |
directorypath |
path to save Output plot. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot data retrieved from UniprotR Function "GetProteinGOInfo".
PlotGoInfo(GOObj , directorypath = NULL)PlotGoInfo(GOObj , directorypath = NULL)
GOObj |
Dataframe retrieved from UniprotR Function "GetProteinGOInfo". |
directorypath |
path to save excel file containig results returened by the function ( default = NA ). |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot data retrieved from UniprotR Function "GetProteinGOInfo".
PlotGoterms(GOObj , directorypath = NULL)PlotGoterms(GOObj , directorypath = NULL)
GOObj |
Dataframe. |
directorypath |
path to save plot returned by function ( default = NA ). |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot proteins gravy index retrieved from "GetSequences" Function.
PlotGravy(SeqDataObjPath , directorypath = NULL)PlotGravy(SeqDataObjPath , directorypath = NULL)
SeqDataObjPath |
Dataframe retrieved from UniprotR Function "GetSequences" |
directorypath |
path to save Output plot. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This function can be used to get a list of UniProt Accession/s from a csv file.
PlotPhysicochemical(SeqDataObjPath , directorypath = NULL)PlotPhysicochemical(SeqDataObjPath , directorypath = NULL)
SeqDataObjPath |
Dataframe returned from GetSequence function. |
directorypath |
Path to save Physcochemical properties plot. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot protein status in the data of the accession/s.
PlotproteinExist(ProteinDataObject,directorypath = NULL)PlotproteinExist(ProteinDataObject,directorypath = NULL)
ProteinDataObject |
input a Dataframe returned from GetMiscellaneous function |
directorypath |
path to save files returened by the function. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot biological process data retrieved from UniprotR Function "GetProteinGOInfo".
PlotProteinGO_bio(GO_df , dir_path = NA)PlotProteinGO_bio(GO_df , dir_path = NA)
GO_df |
Dataframe. |
dir_path |
path to save files returened by the function ( default = NA ). |
if no dir_path was given ( default = NA ) the function will only view the plot and will not save it
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot cellular components data retrieved from UniprotR Function "GetProteinGOInfo".
PlotProteinGO_cel(GO_df , dir_path = NA)PlotProteinGO_cel(GO_df , dir_path = NA)
GO_df |
Dataframe. |
dir_path |
path to save files returened by the function ( default = NA ). |
if no dir_path was given ( default = NA ) the function will only view the plot and Will not save it
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot molecular functions data retrieved from UniprotR Function "GetProteinGOInfo".
PlotProteinGO_molc(GO_df , dir_path = NA)PlotProteinGO_molc(GO_df , dir_path = NA)
GO_df |
Dataframe. |
dir_path |
path to save files returened by the function ( default = NA ). |
if no dir_path was given ( default = NA ) the function will only view the plot and will not save it
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot protein status in the data of the accession/s.
PlotproteinStatus (ProteinDataObject,directorypath = NULL)PlotproteinStatus (ProteinDataObject,directorypath = NULL)
ProteinDataObject |
input a Dataframe returned from GetMiscellaneous function |
directorypath |
path to save files returened by the function. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to plot different taxas found of the accessions.
PlotProteinTaxa(ProteinDataObject , directorypath = NULL)PlotProteinTaxa(ProteinDataObject , directorypath = NULL)
ProteinDataObject |
input a Dataframe of proteins as rownames. |
directorypath |
path to save files returened by the function. |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]
This Function is used to check validty of input accessions the data of the accession/s.
ProcessAcc(Accessions)ProcessAcc(Accessions)
Accessions |
acession list returened from GetAccession function |
Mohmed Soudy [email protected] and Ali Mostafa [email protected]