Closed fifdick closed 5 years ago
fifdick
commented
5 years ago sorry noticed it was my mistake. I have to add motifs and all other kinds of features to the plot. The reason I didnt before is because I intended to make a function to plot various genes of which i dont know prior to plotting, what kind of features I will be able to retrieve. (something elike draw_allFeatures() would be cool, to draw all features that could have been retrieved)
brennanpincardiff
commented
5 years ago Thanks fifdick, If you add the code:
p <- draw_recept_dom(p, prot_data)You will get this picture.
Best wishes, Paul
fifdick
commented
5 years ago yes. I found this too, thank you! Is there anything else I can add (I tried all available functions but thats the only thing that comes up)? Although in the features it shows all those things:
type
featuresTemp CHAIN
featuresTemp.1 TRANSMEM
featuresTemp.2 TRANSMEM
featuresTemp.3 TRANSMEM
featuresTemp.4 TRANSMEM
featuresTemp.5 ZN_FING
featuresTemp.6 MUTAGEN
featuresTemp.7 MUTAGEN
featuresTemp.8 MUTAGEN are they not plotable?
brennanpincardiff
commented
5 years ago Super question, fifdick.
Because Uniprot seems to come up with an almost limitless variation in names, I haven't added each one individually. I should probably add a plot all function which would help, I think.
In the mean time the following code will draw all the features in stages:
library(drawProteins)
prot_data <- drawProteins::get_features("Q9NX47")
# produce data frame
prot_data <- drawProteins::feature_to_dataframe(prot_data)
# make protein schematic
p <- draw_canvas(prot_data)
p <- draw_chains(p, prot_data)
p <- draw_domains(p, prot_data)
p <- draw_recept_dom(p, prot_data)
p
# add ZN_FING block in blue
p <- p + ggplot2::geom_rect(data = prot_data[prot_data$type == "ZN_FING",],
mapping=ggplot2::aes(xmin=begin,
xmax=end,
ymin=order-0.2,
ymax=order+0.2),
fill = "blue")
p
# add ZN_FING label on top of this
p <- p + ggplot2::geom_label(data = prot_data[prot_data$type == "ZN_FING", ],
ggplot2::aes(x = begin + (end-begin)/2,
y = order,
label = description),
size = 3)
p
# add MUTAGEN as red bars on top...
p <- p + ggplot2::geom_rect(data = prot_data[prot_data$type == "MUTAGEN",],
mapping=ggplot2::aes(xmin=begin,
xmax=end,
ymin=order-0.2,
ymax=order+0.2),
colour = "red")
p
Does this help? Best wishes, Paul
fifdick
commented
5 years ago super. thanks a lot for this help! Might come back with another question in the future. Nice package. Its very intuitive and easy to use.
Am Di., 4. Dez. 2018 um 14:48 Uhr schrieb Paul Brennan < notifications@github.com>:
Super question, fifdick.
Because Uniprot seems to come up with an almost limitless variation in names, I haven't added each one individually. I should probably add a plot all function which would help, I think.
In the mean time the following code will draw all the features in stages:
library(drawProteins) prot_data <- drawProteins::get_features("Q9NX47")# produce data frameprot_data <- drawProteins::feature_to_dataframe(prot_data)
make protein schematicp <- draw_canvas(prot_data)p <- draw_chains(p, prot_data)p <- draw_domains(p, prot_data)p <- draw_recept_dom(p, prot_data)p
[image: rplot] https://user-images.githubusercontent.com/7151469/49446035-2a020f80-f7cb-11e8-844f-79b25d246c1c.png
add ZN_FING block in blue
p <- p + ggplot2::geom_rect(data = prot_data[prot_data$type == "ZN_FING",], mapping=ggplot2::aes(xmin=begin, xmax=end, ymin=order-0.2, ymax=order+0.2), fill = "blue") p
[image: query_20181204_1] https://user-images.githubusercontent.com/7151469/49446004-18b90300-f7cb-11e8-9026-b32caebbd9ab.png
add ZN_FING label on top of this
p <- p + ggplot2::geom_label(data = prot_data[prot_data$type == "ZN_FING", ], ggplot2::aes(x = begin + (end-begin)/2, y = order, label = description), size = 3) p
[image: query_20181204_2] https://user-images.githubusercontent.com/7151469/49446017-1e164d80-f7cb-11e8-8937-ba2a22e2026d.png
add MUTAGEN as red bars on top...
p <- p + ggplot2::geom_rect(data = prot_data[prot_data$type == "MUTAGEN",], mapping=ggplot2::aes(xmin=begin, xmax=end, ymin=order-0.2, ymax=order+0.2), colour = "red") p
[image: query_20181204_3] https://user-images.githubusercontent.com/7151469/49446024-22db0180-f7cb-11e8-8d15-afed6ee02fbd.png
Does this help? Best wishes, Paul
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Hi. Im using drawProteins to plot the domains of various genes. As a test i followed the script of this page: http://rforbiochemists.blogspot.com/2018/02/my-drawproteins-package-has-been.html This worked perfectly well. When trying to draw the chains for the gene MARCH5 (https://www.uniprot.org/uniprot/Q9NX47#family_and_domains) Im proceeding as follows: ` prot_data <- drawProteins::get_features("Q9NX47")
produce data frame
`
I get a grey chain with no domains (see attached picture). Although when checking
prot_dataI can see that there are domain features listed:Did I do sth wrong or is there simply not more data to be retrieved?
Thanks in advance
`Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0 LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=en_DK.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_DK.UTF-8 LC_COLLATE=en_DK.UTF-8
[5] LC_MONETARY=en_DK.UTF-8 LC_MESSAGES=en_DK.UTF-8 [7] LC_PAPER=en_DK.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_DK.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] ggplot2_3.1.0 _drawProteins1.2.0
[3] ensembldb_2.6.3 AnnotationFilter_1.6.0 [5] GenomicFeatures_1.34.1 AnnotationDbi_1.44.0 [7] Biobase_2.41.2 GenomicRanges_1.32.4 [9] GenomeInfoDb_1.18.1 IRanges_2.15.16 [11] S4Vectors_0.19.19 BiocGenerics_0.28.0
[13] nvimcom_0.9-58
loaded via a namespace (and not attached):
[1] Rcpp_0.12.18 lattice_0.20-38
[3] prettyunits_1.0.2 Rsamtools_1.33.3
[5] Biostrings_2.49.0 assertthat_0.2.0
[7] digest_0.6.15 R6_2.3.0
[9] plyr_1.8.4 RSQLite_2.1.1
[11] httr_1.3.1 pillar_1.3.0
[13] zlibbioc_1.28.0 rlang_0.3.0.1
[15] progress_1.2.0 lazyeval_0.2.1
[17] curl_3.2 blob_1.1.1
[19] Matrix_1.2-15 labeling_0.3
[21] BiocParallel_1.15.8 stringr_1.3.1
[23] ProtGenerics_1.14.0 RCurl_1.95-4.11
[25] bit_1.1-14 biomaRt_2.38.0
[27] munsell_0.5.0 DelayedArray_0.7.21
[29] compiler_3.5.1 rtracklayer_1.41.3
[31] pkgconfig_2.0.2 tidyselect_0.2.4
[33] SummarizedExperiment_1.10.1 tibble_1.4.2
[35] GenomeInfoDbData_1.2.0 matrixStats_0.54.0
[37] XML_3.98-1.12 withr_2.1.2
[39] crayon_1.3.4 dplyr_0.7.7 [41] GenomicAlignments_1.16.0 bitops_1.0-6 [43] grid_3.5.1 jsonlite_1.5
[45] gtable_0.2.0 DBI_1.0.0
[47] magrittr_1.5 scales_1.0.0 [49] stringi_1.2.4 XVector_0.21.3 [51] bindrcpp_0.2.2 tools_3.5.1
[53] bit64_0.9-7 glue_1.3.0 [55] purrr_0.2.5 hms_0.4.2
[57] colorspace_1.3-2 memoise_1.1.0
[59] bindr_0.1.1 `