Using extract_transcripts in drawProteins (original) (raw)

Making a new dataframe with each transcript separated

The NFkappaB transcription factor family contains two proteins that are present in two forms. The dataframe obtained from Uniprot is contained in the drawProtein package as “five_rel_data” and can be loaded using the data()function.

When loaded this has 320 obs of 9 variables and will plot five chains as shown by checking the max(five_rel_data$order) function.

To plot all the transcripts, a new dataframe is produced using theextact_transcripts() function. The new dataframe is called prot_data and has 430 obs of 9 variables and will plot seven chains as shown by checking the max(prot_data$order) function.

# load up data for five NF-kappaB proteins
data("five_rel_data")
max(five_rel_data$order)

[1] 5

# returns 5

# use extract_transcripts() to create a new data frame
prot_data <- extract_transcripts(five_rel_data)
max(prot_data$order)

[1] 7

# returns 7

Now, let’s check out the chains for the two objects for comparison purposes.

p1 <- draw_canvas(five_rel_data)
p1 <- draw_chains(p1, five_rel_data)
p1 <- p1 + ggtitle("Five chains plotted")

p2 <- draw_canvas(prot_data)
p2 <- draw_chains(p2, prot_data)
p2 <- p2 + ggtitle("Seven chains plotted")

p1

p2

The appropriate domains and phosphorylation sites can be drawn correctly.

p2 <- draw_domains(p2, prot_data)
p2 <- draw_phospho(p2, prot_data, size =8) 
p2

Note that the names of the different transcripts are the same so it’s wise to use the option customize the labels.

p2 <- draw_canvas(prot_data)
p2 <- draw_chains(p2, prot_data,
            fill = "lightsteelblue1", 
            outline = "grey",
            labels = c("p105",
                        "p105",
                        "p100", 
                        "p100",
                        "Rel B",
                        "c-Rel", 
                        "p65/Rel A",
                        "p50",
                        "p52"),
            label_size = 5)
p2 <- draw_phospho(p2, prot_data, size = 8, fill = "red")
p2 + theme_bw()

Session info

Here is the output of sessionInfo() on the system on which this document was compiled:

R version 4.5.0 RC (2025-04-04 r88126)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS

Matrix products: default
BLAS:   /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB              LC_COLLATE=C              
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] knitr_1.50          ggplot2_3.5.2       httr_1.4.7         
[4] drawProteins_1.28.0 BiocStyle_2.36.0   

loaded via a namespace (and not attached):
 [1] gtable_0.3.6        jsonlite_2.0.0      dplyr_1.1.4        
 [4] compiler_4.5.0      BiocManager_1.30.25 Rcpp_1.0.14        
 [7] tidyselect_1.2.1    tinytex_0.57        magick_2.8.6       
[10] jquerylib_0.1.4     scales_1.3.0        yaml_2.3.10        
[13] fastmap_1.2.0       R6_2.6.1            labeling_0.4.3     
[16] generics_0.1.3      curl_6.2.2          tibble_3.2.1       
[19] bookdown_0.43       munsell_0.5.1       bslib_0.9.0        
[22] pillar_1.10.2       rlang_1.1.6         cachem_1.1.0       
[25] xfun_0.52           sass_0.4.10         cli_3.6.4          
[28] withr_3.0.2         magrittr_2.0.3      digest_0.6.37      
[31] grid_4.5.0          lifecycle_1.0.4     vctrs_0.6.5        
[34] evaluate_1.0.3      glue_1.8.0          farver_2.1.2       
[37] colorspace_2.1-1    rmarkdown_2.29      tools_4.5.0        
[40] pkgconfig_2.0.3     htmltools_0.5.8.1