Tables

Let’s build some tables!

Explore your IPR results here

w/ knitr

knitr::kable(head(ipr_combnd), format='html')
AccNum Analysis DB.ID SignDesc StartLoc StopLoc SLength IPRAcc IPRDesc
YP_008530241 Pfam PF17259 Family of unknown function (DUF5325) 4 60 63 IPR035211 Protein of unknown function DUF5325
YP_008530243 Pfam PF01741 Large-conductance mechanosensitive channel, MscL 1 116 120 IPR037673 Large-conductance mechanosensitive channel/anditomin synthesis protein L
YP_498609 Pfam PF11638 DnaA N-terminal domain 5 64 453 IPR024633 DnaA N-terminal domain
YP_498609 Pfam PF00338 Ribosomal protein S10p/S20e 7 101 102 IPR027486 Ribosomal protein S10 domain
YP_498609 Pfam PF08299 Bacterial dnaA protein helix-turn-helix 361 429 453 IPR013159 Chromosomal replication initiator, DnaA C-terminal
YP_498610 Pfam PF00712 DNA polymerase III beta subunit, N-terminal domain 2 128 377 IPR022634 DNA polymerase III, beta sliding clamp, N-terminal

w/ rmarkdown

paged_table(ipr_combnd)

w/ kableExtra

ipr_combnd |>
  head() |>
  kable(caption = "Table 1. Annotate with kableExtra") |>
  kable_styling(c("striped", "hover", "condensed"), full_width = F,
                position = "left") |>
  add_header_above(c("protein"=1, "domains" = 8)) |>
  column_spec(1, bold = T) |>
  row_spec(0, italic = T)
Table 1. Annotate with kableExtra
protein
domains
AccNum Analysis DB.ID SignDesc StartLoc StopLoc SLength IPRAcc IPRDesc
YP_008530241 Pfam PF17259 Family of unknown function (DUF5325) 4 60 63 IPR035211 Protein of unknown function DUF5325
YP_008530243 Pfam PF01741 Large-conductance mechanosensitive channel, MscL 1 116 120 IPR037673 Large-conductance mechanosensitive channel/anditomin synthesis protein L
YP_498609 Pfam PF11638 DnaA N-terminal domain 5 64 453 IPR024633 DnaA N-terminal domain
YP_498609 Pfam PF00338 Ribosomal protein S10p/S20e 7 101 102 IPR027486 Ribosomal protein S10 domain
YP_498609 Pfam PF08299 Bacterial dnaA protein helix-turn-helix 361 429 453 IPR013159 Chromosomal replication initiator, DnaA C-terminal
YP_498610 Pfam PF00712 DNA polymerase III beta subunit, N-terminal domain 2 128 377 IPR022634 DNA polymerase III, beta sliding clamp, N-terminal

You can search, sort, and query the table interactively.

w/ DT, datatable

ipr_combnd |>
  head() |> 
  datatable(fillContainer=FALSE,
            options=list(pageLength=8))

adding extensions

You can now show/hide specific columns using the Column visibility button.

DT::datatable(ipr_combnd,
              extensions = c('Buttons', 'FixedColumns',
                             'RowReorder', 'RowGroup'),
              options = list(
                pageLength = 5,
                dom = 'Bfrtip',
                buttons = I('colvis'),
                buttons=list(list(extend = 'colvis', columns = c(5:9))),
                fixedColumns = list(leftColumns = 2),
                fixedHeader = TRUE,
                rowReorder = TRUE, order = list(c(0, 'asc')),
                scrollX = TRUE,
                rowGroup = list(dataSrc = 1),
                lengthMenu = c(10, 25, 100)
              ))

w/ gt

ipr_combnd |>
  head() |> 
  gt()
AccNum Analysis DB.ID SignDesc StartLoc StopLoc SLength IPRAcc IPRDesc
YP_008530241 Pfam PF17259 Family of unknown function (DUF5325) 4 60 63 IPR035211 Protein of unknown function DUF5325
YP_008530243 Pfam PF01741 Large-conductance mechanosensitive channel, MscL 1 116 120 IPR037673 Large-conductance mechanosensitive channel/anditomin synthesis protein L
YP_498609 Pfam PF11638 DnaA N-terminal domain 5 64 453 IPR024633 DnaA N-terminal domain
YP_498609 Pfam PF00338 Ribosomal protein S10p/S20e 7 101 102 IPR027486 Ribosomal protein S10 domain
YP_498609 Pfam PF08299 Bacterial dnaA protein helix-turn-helix 361 429 453 IPR013159 Chromosomal replication initiator, DnaA C-terminal
YP_498610 Pfam PF00712 DNA polymerase III beta subunit, N-terminal domain 2 128 377 IPR022634 DNA polymerase III, beta sliding clamp, N-terminal
 
ipr_gt <- ipr_combnd |>
  group_by(AccNum) |> 
  gt() |> 
  tab_header(title=md("IPRScan Results"), subtitle="using GT") |>
  tab_source_note(md("More information on the [GT package](https://gt.rstudio.com/index.html).")) |> 
  cols_align(align="right", columns=TRUE) |> 
  tab_spanner(label="Protein", columns=matches("AccNum")) |> 
  tab_spanner(label="Domains", columns=matches("Analysis|DB.ID|SignDesc")) |> 
  tab_spanner(label="DomLoc", columns=matches("Loc|Length")) |>
  tab_spanner(label="IPR", columns=matches("IPR")) |>
  tab_options(
    # Headings; Titles
        heading.background.color="#3C5488",
        heading.border.bottom.color="#989898",
        heading.title.font.size="12px",
        heading.subtitle.font.size="11px",
        # Column labels
        column_labels.background.color="#4DBBD5", #B09C85FF
        column_labels.font.size="12px",
        # Stubs
        stub.background.color="#4DBBD5", #B09C85FF
        stub.border.style="dashed",
        stub.border.color="#989898",
        stub.border.width="1px",
        # Row groups
        row_group.background.color="coral3", #FFEFDB80
        row_group.border.top.color="#989898",
        row_group.border.bottom.style="none",
        row_group.font.size="12px",
        # Summary rows
        summary_row.border.color="#989898",
        # summary_row.background.color="#FFEBEE",
        # grand_summary_row.background.color="#FFFFFF",
        # Table
        table.font.color="#323232",
        table_body.hlines.color="#989898",
        table_body.border.top.color="#989898",
        table.font.size="10px",
        table.width="80%")
Warning: Since gt v0.3.0, `columns = TRUE` has been deprecated.
• Please use `columns = everything()` instead.
ipr_gt
IPRScan Results
using GT
Domains DomLoc IPR
Analysis DB.ID SignDesc StartLoc StopLoc SLength IPRAcc IPRDesc
YP_008530241
Pfam PF17259 Family of unknown function (DUF5325) 4 60 63 IPR035211 Protein of unknown function DUF5325
YP_008530243
Pfam PF01741 Large-conductance mechanosensitive channel, MscL 1 116 120 IPR037673 Large-conductance mechanosensitive channel/anditomin synthesis protein L
YP_498609
Pfam PF11638 DnaA N-terminal domain 5 64 453 IPR024633 DnaA N-terminal domain
Pfam PF00338 Ribosomal protein S10p/S20e 7 101 102 IPR027486 Ribosomal protein S10 domain
Pfam PF08299 Bacterial dnaA protein helix-turn-helix 361 429 453 IPR013159 Chromosomal replication initiator, DnaA C-terminal
YP_498610
Pfam PF00712 DNA polymerase III beta subunit, N-terminal domain 2 128 377 IPR022634 DNA polymerase III, beta sliding clamp, N-terminal
Pfam PF00308 Bacterial dnaA protein 117 332 453 IPR013317 Chromosomal replication initiator protein DnaA
Pfam PF02767 DNA polymerase III beta subunit, central domain 137 251 377 IPR022637 DNA polymerase III, beta sliding clamp, central
YP_498611
Pfam PF02768 DNA polymerase III beta subunit, C-terminal domain 254 375 377 IPR022635 DNA polymerase III, beta sliding clamp, C-terminal
YP_498612
Pfam PF13275 S4 domain 14 64 81 - -
YP_498613
Pfam PF02463 RecF/RecN/SMC N terminal domain 3 347 370 IPR003395 RecF/RecN/SMC, N-terminal
Pfam PF00204 DNA gyrase B 232 401 644 IPR013506 DNA topoisomerase, type IIA, subunit B, domain 2
Pfam PF01751 Toprim domain 430 541 644 IPR006171 TOPRIM domain
Pfam PF00986 DNA gyrase B subunit, carboxyl terminus 574 634 644 IPR002288 DNA gyrase B subunit, C-terminal
YP_498614
Pfam PF00521 DNA gyrase/topoisomerase IV, subunit A 33 473 887 IPR002205 DNA topoisomerase, type IIA, domain A
Pfam PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase 40 180 644 IPR003594 Histidine kinase/HSP90-like ATPase
Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller 507 550 887 IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller 614 658 887 IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller 661 706 887 IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller 713 754 887 IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller 764 810 887 IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
YP_498615
Pfam PF03989 DNA gyrase C-terminal domain, beta-propeller 556 605 887 IPR006691 DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat
YP_498616
Pfam PF01256 Carbohydrate kinase 1 225 233 IPR000631 ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase
YP_498617
Pfam PF00221 Aromatic amino acid lyase 10 470 504 IPR001106 Aromatic amino acid lyase
Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 223 400 428 IPR002314 Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)
YP_498618
Pfam PF02403 Seryl-tRNA synthetase N-terminal domain 1 107 428 IPR015866 Serine-tRNA synthetase, type1, N-terminal
YP_498619
Pfam PF03591 AzlC protein 16 156 231 IPR011606 Branched-chain amino acid transport, permease
YP_498620
Pfam PF05437 Branched-chain amino acid transport protein (AzlD) 8 106 109 IPR008407 Branched-chain amino acid transport, AzlD
YP_498621
Pfam PF00561 alpha/beta hydrolase fold 38 302 322 IPR000073 Alpha/beta hydrolase fold-1
YP_498622
Pfam PF09991 Predicted membrane protein (DUF2232) 20 298 312 IPR018710 Protein of unknown function DUF2232
Pfam PF01368 DHH family 337 494 655 IPR001667 DDH domain
YP_498623
Pfam PF03948 Ribosomal protein L9, C-terminal domain 65 148 150 IPR020069 Ribosomal protein L9, C-terminal
Pfam PF02272 DHHA1 domain 516 645 655 IPR003156 DHHA1 domain
YP_498624
Pfam PF01281 Ribosomal protein L9, N-terminal domain 1 49 150 IPR020070 Ribosomal protein L9, N-terminal
Pfam PF03796 DnaB-like helicase C terminal domain 185 457 466 IPR007694 DNA helicase, DnaB-like, C-terminal
YP_498625
Pfam PF00772 DnaB-like helicase N terminal domain 10 110 466 IPR007693 DNA helicase, DnaB-like, N-terminal
YP_498626
Pfam PF00709 Adenylosuccinate synthetase 5 420 427 IPR001114 Adenylosuccinate synthetase
Pfam PF00072 Response regulator receiver domain 5 114 233 IPR001789 Signal transduction response regulator, receiver domain
YP_498627
Pfam PF00486 Transcriptional regulatory protein, C terminal 153 229 233 IPR001867 OmpR/PhoB-type DNA-binding domain
Pfam PF13426 PAS domain 274 368 608 IPR000014 PAS domain
Pfam PF00512 His Kinase A (phospho-acceptor) domain 376 441 608 IPR003661 Signal transduction histidine kinase, dimerisation/phosphoacceptor domain
Pfam PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase 487 598 608 IPR003594 Histidine kinase/HSP90-like ATPase
YP_498628
Pfam PF00672 HAMP domain 201 252 608 IPR003660 HAMP domain
YP_498629
Pfam PF07435 YycH protein 1 424 427 IPR009996 Regulatory protein YycH
YP_498630
Pfam PF09648 YycI protein 38 253 262 IPR018604 Regulatory protein YycH-like
YP_498633
Pfam PF00753 Metallo-beta-lactamase superfamily 14 220 266 IPR001279 Metallo-beta-lactamase
YP_498636
Pfam PF02590 Predicted SPOUT methyltransferase 1 158 159 IPR003742 RNA methyltransferase RlmH
YP_498637
Pfam PF19614 Family of unknown function (DUF6119) 29 479 581 IPR026487 Sporadically distributed protein CHP04141
YP_498639
Pfam PF01207 Dihydrouridine synthase (Dus) 11 137 150 IPR035587 DUS-like, FMN-binding domain
YP_498640
Pfam PF01925 Sulfite exporter TauE/SafE 10 247 251 IPR002781 Transmembrane protein TauE-like
YP_498641
Pfam PF02583 Metal-sensitive transcriptional repressor 4 83 86 IPR003735 Metal-sensitive transcriptional repressor
Pfam PF01206 Sulfurtransferase TusA 120 188 355 IPR001455 TusA-like domain
Pfam PF13686 DsrE/DsrF/DrsH-like family 201 354 355 IPR032836 DsrE2-like family
YP_498642
Pfam PF00753 Metallo-beta-lactamase superfamily 13 168 444 IPR001279 Metallo-beta-lactamase
Pfam PF00581 Rhodanese-like domain 15 98 355 IPR001763 Rhodanese-like domain
Pfam PF00581 Rhodanese-like domain 359 439 444 IPR001763 Rhodanese-like domain
More information on the GT package.