Package drawproteins

Transcription

1 Package drawproteins June 5, 2018 Title Package to Draw Protein Schematics from Unirot API outut Version This ackage draws rotein schematics from Unirot API outut. From the JSON returned by the GET command, it creates a frame from the Unirot Features API. This frame can then be used by geoms based on gglot2 and base R to draw rotein schematics. Deends R (>= 3.4) License MIT + file LICENSE Encoding UTF-8 LazyData false Imorts gglot2, httr, dlyr Suggests covr, testthat, knitr, rmarkdown, BiocStyle VignetteBuilder knitr RoxygenNote URL htts://github.com/brennanincardiff/drawproteins BugReorts htts://github.com/brennanincardiff/drawproteins/issues/new biocviews Visualization, FunctionalPrediction, Proteomics Author Paul Brennan [aut, cre] Maintainer Paul Brennan <brennanincardiff@gmail.com> R toics documented: drawproteins draw_canvas draw_chains draw_domains draw_motif draw_hosho draw_recet_dom draw_regions draw_reeat extract_feat_acc extract_names extract_transcrits

2 2 draw_canvas feature_to_frame five_rel_ five_rel_list get_features hosho_site_info rotein_json rel_a_features rel_json tnfs_ Index 17 drawproteins drawproteins. drawproteins. draw_canvas Create gglot2 object with rotein chains from feature base draw_canvas uses the frame containing the rotein features to creates the basic lot element by determining the length of the longest rotein. draw_canvas( = ) Dataframe of one or more rows with the following column names: tye, descrition, Must contain a minimum of one "CHAIN" as $tye. A gglot2 object either in the lot window or as an object. Examles # draws a blank canvas of the correct size draw_canvas(five_rel_) # combines with draw_chains to lot and label chains. <- draw_canvas(five_rel_) <- draw_chains(, five_rel_)

3 draw_chains 3 draw_chains Create gglot2 object with rotein chains from feature base draw_chains uses the frame containing the rotein features to lot the chains, the full length roteins. It creates the basic lot element by determining the length of the longest rotein. The gglot2 function geom_rect is then used to draw each of the rotein chains roortional to their number of amino acids (length). draw_chains(, =, outline = "black", fill = "grey", label_chains = TRUE, labels = [$tye == "CHAIN", ]$entryname, size = 0.5, label_size = 4) outline fill label_chains labels size label_size gglot2 object ideally created with draw_canvas. Dataframe of one or more rows with the following column names: tye, descrition, Must contain a minimum of one "CHAIN" as $tye. Colour of the outline of each chain. Colour of the fill of each chain. Otion to label chains or not. Vector with source of names for the chains. EntryName used as default but can be changed. Size of the outline of the chains. Size of the text used for labels. A gglot2 object either in the lot window or as an object. Examles # combines with draw_canvas to lot and label chains. <- draw_canvas(five_rel_) <- draw_chains(, five_rel_) # draws five chains with different colours to default <- draw_canvas(five_rel_) draw_chains(, five_rel_, label_chains = FALSE, fill = "red", outline = "grey")

4 4 draw_domains # combines with draw_chains to lot chains and domains. <- draw_canvas(five_rel_) <- draw_chains(, five_rel_, label_size = 1.25) <- draw_regions(, five_rel_) draw_domains Add rotein domains to gglot2 object. draw_domains adds domains to the gglot2 object created by draw_chains. It uses the object. The gglot2 function geom_rect is used to draw each of the domain chains roortional to their number of amino acids (length). draw_domains(, =, label_domains = TRUE, label_size = 4, show.legend = TRUE) label_domains label_size show.legend gglot2 object ideally created with draw_canvas. Dataframe of one or more rows with the following column names: tye, descrition, Must contain a minimum of one "CHAIN" as $tye. Otion to label domains or not. Size of the text used for labels. Otion to include legend in this layer A gglot2 object either in the lot window or as an object with an additional geom_rect layer. Examles # combines with draw_chains to lot chains and domains. <- draw_canvas(five_rel_) <- draw_chains(, five_rel_, label_size = 1.25) <- draw_domains(, five_rel_)

5 draw_motif 5 draw_motif Add rotein motifs sites to gglot2 object. draw_motif adds rotein motifs from Unirot to gglot2 object created by draw_canvas and draw_chains. It uses the object. The gglot2 function geom_rect is used to draw each of the motifs roortional to their number of amino acids (length). draw_motif(, =, show.legend = TRUE) show.legend gglot2 object ideally created with draw_canvas. Dataframe of one or more rows with the following column names: tye, descrition, Must contain a minimum of one "CHAIN" as $tye. Otion to include legend in this layer A gglot2 object either in the lot window or as an object with an additional geom_rect layer. Examles # combines with draw_chains to lot chains and motifs <- draw_canvas(five_rel_) <- draw_chains(, five_rel_, label_size = 1.25) <- draw_motif(, five_rel_) draw_hosho Add rotein hoshorylation sites to gglot2 object. draw_hosho adds hoshorylation sites to gglot2 object created by draw_canvas and draw_chains. It uses the object. The gglot2 function geom_oint is used to draw each of the hoshorylation sites at their location as determined by object. draw_hosho(, =, size = 2, fill = "yellow", show.legend = FALSE)

6 6 draw_recet_dom size fill show.legend gglot2 object ideally created with draw_canvas. Dataframe of one or more rows with the following column names: tye, descrition, Must contain a minimum of one "CHAIN" as $tye. Size of the circle Colour of the circle. Otion to include legend in this layer A gglot2 object either in the lot window or as an object with an additional geom_oint layer. Examles # combines will with draw_domains to lot chains and hoshorylation sites. <- draw_canvas(five_rel_) <- draw_chains(, five_rel_, label_size = 1.25) <- draw_hosho(, five_rel_) draw_recet_dom Add recetor domains to gglot2 object. draw_recet_dom adds recetor domains to the gglot2 object created by draw_chains. It uses the object. The gglot2 function geom_rect is used to draw each of the domain chains roortional to their number of amino acids (length). draw_recet_dom(, =, label_domains = FALSE, label_size = 4, show.legend = TRUE) label_domains label_size show.legend gglot2 object ideally created with draw_canvas. Dataframe of one or more rows with the following column names: tye, descrition, Uses TOPO_DOM and TRANSMEM tye to lot these arts of recetors Otion to label recetor domains or not. Size of the text used for labels. Otion to include legend in this layer A gglot2 object either in the lot window or as an object with an additional geom_rect layer.

7 draw_regions 7 Examles # combines with draw_chains to lot chains and domains. ("tnfs_") <- draw_canvas(tnfs_) <- draw_chains(, tnfs_, label_size = 1.25) <- draw_recet_dom(, tnfs_) # we like to draw recetors vertically so fli using gglot2 functions + gglot2::scale_x_reverse() + gglot2::coord_fli() draw_regions Add rotein region sites to gglot2 object. draw_regions adds rotein regions from Unirot to gglot2 object created by draw_canvas draw_chains. It uses the object. The gglot2 function geom_rect is used to draw each of the regions roortional to their number of amino acids (length). draw_regions(, =, show.legend = TRUE) show.legend gglot2 object ideally created with draw_canvas. Dataframe of one or more rows with the following column names: tye, descrition, Must contain a minimum of one "CHAIN" as $tye. Otion to include legend in this layer A gglot2 object either in the lot window or as an object with an additional geom_rect layer. Examles # combines with draw_chains to lot chains and regions. <- draw_canvas(five_rel_) <- draw_chains(, five_rel_, label_size = 1.25) <- draw_regions(, five_rel_)

8 8 draw_reeat draw_reeat Add rotein reeats sites to gglot2 object. draw_reeat adds rotein reeats from Unirot to gglot2 object created by draw_canvas and draw_chains. It uses the object. The gglot2 function geom_rect is used to draw each of the motifs roortional to their number of amino acids (length). draw_reeat(, =, label_size = 2, outline = "dimgrey", fill = "dimgrey", label_reeats = TRUE, show.legend = TRUE) label_size outline fill label_reeats show.legend gglot2 object ideally created with draw_canvas. Dataframe of one or more rows with the following column names: tye, descrition, Must contain a minimum of one "CHAIN" as $tye. Size of text used for labels of rotein reeats. Colour of the outline of each reeat. Colour of the fill of each reeat. Otion to label reeats or not. Otion to include legend in this layer A gglot2 object either in the lot window or as an object with an additional geom_rect layer. Examles # combines with draw_chains to lot chains and reeats. <- draw_canvas(five_rel_) <- draw_chains(, five_rel_, label_size = 1.25) <- draw_reeat(, five_rel_)

9 extract_feat_acc 9 extract_feat_acc Create a frame of rotein features from JSON object (List of 6) Converts the list of 6 JSON object created by getting the features from UniProt. Used in the feature_to_frame(). Does not give order. Does not oerate on List of lists - just the list of 6. extract_feat_acc(features_list) features_list A JSON object - list of 6 with features inside. Created as one of the lists in the list of lists by the get_features() function. A frame with features: "tye", "descrition", "begin", "end" and adds accession, entryname and taxid for each row. Examles ("five_rel_list") one_rotein_features <- extract_feat_acc(five_rel_list[[1]]) head(one_rotein_features) extract_names Extract rotein names into a list Extracts rotein names from JSON object roduced by a search of Unirot with a single rotein asking for all the information. The search roduces a Large list that contains all the Unirot information about a rotein. extract_names(rotein_json) rotein_json A JSON object from a search with 14 rimary arts A List of 6 with "accession", "name", "rotein.recommendedname.fullname", gene.name.rimary, gene.name.synonym and organism.name.scientific

10 10 extract_transcrits Examles # using internal ("rotein_json") rot_names <- extract_names(rotein_json) # generates a list of 6 ## Not run: # access the Unirot Protein API unirot_acc <- c("q04206") # change this for your fav rotein # Get UniProt entry by accession acc_unirot_url <- c("htts:// comb_acc_ai <- aste0(acc_unirot_url, unirot_acc) # basic function is GET() which accesses the API # requires internet access rotein <- httr::get(comb_acc_ai, accet_json()) status_code(rotein) # returns a 200 means it worked # use content() function from httr to give us a list rotein_json <- httr::content(rotein) # gives a Large list # with 14 rimary arts and lots of bits inside # function from my ackage to extract names of rotein names <- extract_names(rotein_json) ## End(Not run) extract_transcrits Create a new frame of rotein features from frame with multile transcrits searated so that each transcrit is drawn seartely with only the aroriate features. This function works on the object returned by the get_features() function. It creates a.frame of features and includes the accession number AND an order number. It uses the extract_feat_acc function extract_transcrits() Dataframe of one or more rows with the following column names: tye, descrition, Must contain a minimum of one "CHAIN" as $tye. A frame with extra rows if there were multile transcrits resent. Extra transcrits will have an order at the end of the object Each new row should have 9 variables including tye, descrition, begin, end, length, accession, entryname, taxid and order for lotting.

11 feature_to_frame 11 Examles (five_rel_) new_ <- extract_transcrits(five_rel_) # because there are two entries with two transcrits max(new_$order) # should now be 7... feature_to_frame Create a frame of rotein features from JSON object This function works on the object returned by the get_features() function. It creates a.frame of features and includes the accession number AND an order number. It uses the extract_feat_acc function below. feature_to_frame(features_in_lists_of_six) features_in_lists_of_six A list of lists returned by get_features() The number of lists corresonds to the number of accession numbers queried using get_features. The list of 6 contains rotein names and features. A frame with 9 variables including tye, descrition, begin, end, length, accession, entryname, taxid and order for lotting. Examles ("rel_json") rel_ <- feature_to_frame(rel_json) head(rel_) ("five_rel_list") rot_ <- feature_to_frame(five_rel_list) head(rot_)

12 12 five_rel_list five_rel_ Dataframe features of 5 human NFkaaB roteins Unirot on 1 Nov 2017 Dataframe features of 5 human NFkaaB roteins Unirot on 1 Nov 2017 five_rel_ Format A frame with 320 rows and 9 variables: tye tye of features - e.g. chain descrition long name for the rotein begin starting osition (amino acid number) of feature end ending osition (amino acid number) of feature length length of feature - number of amino acids accession rotein Unirot accession number entryname rotein Unirot entry Name taxid taxonomic identification - secies order lotting order from the bottom of the grah A frame with 320 rows and 9 variables Source Unirot htt:// Accession numbers Q04206 Q01201 Q04864 P19838 Q00653 five_rel_list Features of five human Rel A roteins List of features from five human NFkaaB roteins downloaded from Unirot on 15 August 2017 five_rel_list Format Large List of 5 elements - one element for each rotein

13 get_features 13 Large List of 5 elements - one element for each rotein Source Unirot htt:// Accession numbers Q04206 Q01201 Q04864 P19838 Q00653 get_features GET features of rotein(s) from UniProt API This function creates the URL required to query the UniProt API and returns the features of the rotein or roteins in JSON format. It uses the GET() function from the httr ackage. get_features(roteins_acc) roteins_acc A vector of length 1 with one or more UniProt accession numbers searated by saces. If there is internet access and the UniProt accession numbers are good, the function will return a list of lists. The list will be of length equivalent to the number of Unirot accession numbers sulied. The lists inside will be of length 6 and will contain information about the roteins and the features. Examles # Requires internet access rot_ <- get_features("q04206 Q01201 Q04864 P19838 Q00653") hosho_site_info Create a frame of rotein features from JSON object Reduces.frame of features to just hoshorylation sites. Uses a subsetting ste and a gre with the attern "Phosho". hosho_site_info(features)

14 14 rotein_json features A frame of rotein features, for examle created by the feature_to_frame() function. A frame that only contains rotein hoshorylation sites from Unirot Examles sites <- hosho_site_info(five_rel_) head(sites) rotein_json Unirot infor human Rel A rotein in JSON format Large list (968.8 Kb) of information about human Rel A downloaded from Unirot on 1 November 2017 rotein_json Format List of 1 with List of 14 inside List of 6 - information necessary to draw Rel A/65 Source htt://

15 rel_a_features 15 rel_a_features Features of human Rel A rotein List of features from human Rel A downloaded from Unirot on 15 August 2017 rel_a_features Format List of 6 - information necessary to draw Rel A/65 List of 6 - information necessary to draw Rel A/65 Source htt:// rel_json Human Rel A rotein features in JSON format List of 1 with List of 6 inside downloaded from Unirot on 1 November 2017 rel_json Format List of 1 with List of 6 - information necessary to draw Rel A/65 List of 1 with List of 6 - information necessary to draw Rel A/65 Source htt://

16 16 tnfs_ tnfs_ Dataframe features of 2 human TNF recetors from Unirot on 3 Jan 2018 Dataframe features of 2 human TNF recetors from Unirot on 3 Jan 2018 tnfs_ Format A frame with 127 rows of 9 variables: tye tye of features - e.g. chain descrition long name for the rotein begin starting osition (amino acid number) of feature end ending osition (amino acid number) of feature length length of feature - number of amino acids accession rotein Unirot accession number entryname rotein Unirot entry Name taxid taxonomic identification - secies order lotting order from the bottom of the grah A frame with 127 rows and 9 variables Source Unirot htt:// Accession numbers P19438 P25942

17 Index Toic sets five_rel_, 12 five_rel_list, 12 rotein_json, 14 rel_a_features, 15 rel_json, 15 tnfs_, 16 draw_canvas, 2, 3 8 draw_chains, 3, 4 8 draw_domains, 4 draw_motif, 5 draw_hosho, 5 draw_recet_dom, 6 draw_regions, 7 draw_reeat, 8 drawproteins, 2 drawproteins-ackage (drawproteins), 2 extract_feat_acc, 9 extract_names, 9 extract_transcrits, 10 feature_to_frame, 11 five_rel_, 12 five_rel_list, 12 geom_oint, 5 get_features, 13 hosho_site_info, 13 rotein_json, 14 rel_a_features, 15 rel_json, 15 tnfs_, 16 17