Merge pull request #9 from hsmaan/release

hsmaan · web-flow · commit e0964c0dbf85 · 2020-05-12T03:44:07.000-04:00
v0.2 update
diff --git a/R/global.R b/R/global.R
@@ -1,6 +1,5 @@
 library(Biostrings)
 library(DECIPHER)
-library(stringi)
 library(stringr)
 library(ape)
 library(igraph)
diff --git a/README.Rmd b/README.Rmd
@@ -19,7 +19,7 @@ knitr::opts_chunk$set(
 
 ## Overview
 
-[The Covid-19 Genotyping Tool](https://hsmaan.shinyapps.io/CovidGenotyper/) (CGT) is an R-Shiny based web application that allows researchers to upload fasta sequences of Covid-19 viral genomes and compare with public sequence data available on [GISAID](https://www.gisaid.org/). Genomic distance is visualized using manifold projection and network analysis, and genotype information with respective to high-prevalence SNPs is determined.
+[The Covid-19 Genotyping Tool](covidgenotyper.app) (CGT) is an R-Shiny based web application that allows researchers to upload fasta sequences of Covid-19 viral genomes and compare with public sequence data available on [GISAID](https://www.gisaid.org/). Genomic distance is visualized using manifold projection and network analysis, and genotype information with respective to high-prevalence SNPs is determined.
 
 ## Details and methodology
 
@@ -29,11 +29,11 @@ The CGT application was developed using the `shiny` R package and framework. Vis
 
 #### Sequence and metadata retrieval 
 
-Processed fasta files of Covid-19 viral genome sequence are retrieved from the  [GISAID](https://www.gisaid.org/) EpiCoV database, which is a public database for sharing of viral genome sequence data. Metadata for GISAID viral genomes are obtained from [nextstrain's ncov build](https://github.com/nextstrain/ncov/blob/master/data/metadata.tsv). Viral genome data and metadata are updated on a weekly basis.
+Processed fasta files and metadata of Covid-19 viral genome sequence are retrieved from the  [GISAID](https://www.gisaid.org/) EpiCoV database, which is a public database for sharing of viral genome sequence data. Viral genome data and metadata are updated on a weekly basis.
 
 #### Genome sequence alignment
 
-GISAID sequences are subset for those that have metadata from nextstrain. Public sequencing data is pre-aligned before being uploaded to the server. Fasta sequences are read and written using the `Biostrings` package. Gap removal and multiple-sequence alignment is performed using `DECIPHER`. Post alignment processing is done using `ape`. User uploaded fasta sequences are processed similarly, with the exception of complete alignment - the user sequence is aligned to the pre-aligned public data profile using `AlignProfiles` from `DECIPHER`.
+GISAID sequences are subset for those that have corresponding metadata. Public sequencing data is pre-aligned before being uploaded to the server. Fasta sequences are read and written using the `Biostrings` package. Gap removal and multiple-sequence alignment is performed using `DECIPHER`. Post alignment processing is done using `ape`. User uploaded fasta sequences are processed similarly, with the exception of complete alignment - the user sequence is aligned to the pre-aligned public data profile using `AlignProfiles` from `DECIPHER`.
 
 #### DNA distance 
 
@@ -66,7 +66,7 @@ Genotype profiles of viral genomes are determined using high prevalence non-syno
 
 CGT can also be installed locally. Application deployment has currently only been tested on Linux systems including Ubuntu 18.04 LTS and Debian 9.0 LTS, thus we only provide installation instructions for Debian/Ubuntu systems. 
 
-##### 1) Installing CGT dependencies
+#### 1) Installing CGT dependencies
 
 Clone the repository locally <br/> 
 `git clone https://github.com/hsmaan/CovidGenotyper`
@@ -94,9 +94,9 @@ cd CovidGenotyper/bin
 Rscript --verbose packages_install.R
 ```
 
-##### 2) Run preprocessing scripts
+#### 2) Run preprocessing scripts
 
-CGT relies on pre-processing plot data prior to deployment to ensure visualizations can be loaded quickly. Fasta sequences should be downloaded from [GISAID's EpiCoV database](https://www.gisaid.org/) and saved as `gisaid_cov2020_sequences_[mmm_dd].fasta` in the `data` folder. Metadata from [nextstrain's ncov repository](https://github.com/nextstrain/ncov) should be saved as `gisaid_metadata_[mmm_dd].tsv`, also in the `data` folder. 
+CGT relies on pre-processing plot data prior to deployment to ensure visualizations can be loaded quickly. Fasta sequences should be downloaded from [GISAID's EpiCoV database](https://www.gisaid.org/) and saved as `gisaid_cov2020_sequences_[mmm_dd].fasta` in the `data` folder. Metadata from GISAID should be saved as `gisaid_metadata_[mmm_dd].tsv`, also in the `data` folder. 
 
 The order for processing scripts is the following:
 
@@ -109,7 +109,7 @@ Rscript --verbose maf_sites_out.R
 Rscript --verbose preprocess_plot_data.R
 ``` 
 
-##### 3) Deploy CGT
+#### 3) Deploy CGT
 
 Now that the shiny application dependencies have been installed and data has been preloaded, the shiny app can be deployed in a variety of ways, documented [here](https://shiny.rstudio.com/deploy/).
 
@@ -146,6 +146,17 @@ docker run --rm cgt/app
 * ggplot2 v3.3.0
 * ggnetwork v0.5.8
 * plotly v4.9.2.1 
+* Cairo v1.5.11
+* intergraph v2.0.2
+* tidyverse v1.3.0
+* data.table v1.12.8
+* stringr v1.4.0
+* reshape2 v1.4.3
+* dplyr v0.8.5
+* parallel v3.6.3
+* ggthemes v4.2.0
+* RColorBrewer v1.1.2
+* GenomicRanges v1.38.0
 
 #### Command-line tools
 
@@ -155,7 +166,6 @@ docker run --rm cgt/app
 
 ## References
 
-* Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. NextStrain: Real-time tracking of pathogen evolution. Bioinformatics. 2018;34(23):4121–3.
 * Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Challenges. 2017;1(1):33–46.
 * Chang W, Cheng J, Allaire JJ, Xie Y, McPherson J. Shiny: Web Application Framework for R. R package version 1.4.0.2. 2020. Available from: https://CRAN.R-project.org/package=shiny
 * Wickham H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
@@ -173,6 +183,20 @@ and shiny. Chapman and Hall/CRC Florida, 2020.
 * Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb genomics. 2016;2(4):e000056.
 * Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012.
 * Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8. 
+* Simon Urbanek and Jeffrey Horner (2020). Cairo: R Graphics Device using Cairo Graphics
+Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG,
+PostScript) and Display (X11 and Win32) Output. R package version 1.5-11.
+https://CRAN.R-project.org/package=Cairo
+* Bojanowski, Michal (2015) intergraph: Coercion Routines for Network Data Objects. R package version 2.0-2. http://mbojan.github.io/intergraph
+* Wickham et al., (2019). Welcome to the tidyverse. Journal of Open Source Software, 4(43), 1686, https://doi.org/10.21105/joss.01686
+* Matt Dowle and Arun Srinivasan (2019). data.table: Extension of `data.frame`. R package version 1.12.8. https://CRAN.R-project.org/package=data.table
+* Hadley Wickham (2019). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.4.0. https://CRAN.R-project.org/package=stringr
+* Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20. URL http://www.jstatsoft.org/v21/i12/.
+* Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2020). dplyr: A Grammar of Data Manipulation. R package version 0.8.5. https://CRAN.R-project.org/package=dplyr
+* R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
+* Jeffrey B. Arnold (2019). ggthemes: Extra Themes, Scales and Geoms for 'ggplot2'. R package version 4.2.0. https://CRAN.R-project.org/package=ggthemes
+* Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes. R package version 1.1-2. https://CRAN.R-project.org/package=RColorBrewer
+* Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi:10.1371/journal.pcbi.1003118
 
 ## License 
 
diff --git a/README.md b/README.md
@@ -5,8 +5,7 @@
 
 ## Overview
 
-[The Covid-19 Genotyping
-Tool](https://hsmaan.shinyapps.io/CovidGenotyper/) (CGT) is an R-Shiny
+[The Covid-19 Genotyping Tool](covidgenotyper.app) (CGT) is an R-Shiny
 based web application that allows researchers to upload fasta sequences
 of Covid-19 viral genomes and compare with public sequence data
 available on [GISAID](https://www.gisaid.org/). Genomic distance is
@@ -30,23 +29,21 @@ processing time (see below).
 
 #### Sequence and metadata retrieval
 
-Processed fasta files of Covid-19 viral genome sequence are retrieved
-from the [GISAID](https://www.gisaid.org/) EpiCoV database, which is a
-public database for sharing of viral genome sequence data. Metadata for
-GISAID viral genomes are obtained from [nextstrain’s ncov
-build](https://github.com/nextstrain/ncov/blob/master/data/metadata.tsv).
+Processed fasta files and metadata of Covid-19 viral genome sequence are
+retrieved from the [GISAID](https://www.gisaid.org/) EpiCoV database,
+which is a public database for sharing of viral genome sequence data.
 Viral genome data and metadata are updated on a weekly basis.
 
 #### Genome sequence alignment
 
-GISAID sequences are subset for those that have metadata from
-nextstrain. Public sequencing data is pre-aligned before being uploaded
-to the server. Fasta sequences are read and written using the
-`Biostrings` package. Gap removal and multiple-sequence alignment is
-performed using `DECIPHER`. Post alignment processing is done using
-`ape`. User uploaded fasta sequences are processed similarly, with the
-exception of complete alignment - the user sequence is aligned to the
-pre-aligned public data profile using `AlignProfiles` from `DECIPHER`.
+GISAID sequences are subset for those that have corresponding metadata.
+Public sequencing data is pre-aligned before being uploaded to the
+server. Fasta sequences are read and written using the `Biostrings`
+package. Gap removal and multiple-sequence alignment is performed using
+`DECIPHER`. Post alignment processing is done using `ape`. User uploaded
+fasta sequences are processed similarly, with the exception of complete
+alignment - the user sequence is aligned to the pre-aligned public data
+profile using `AlignProfiles` from `DECIPHER`.
 
 #### DNA distance
 
@@ -117,7 +114,7 @@ only been tested on Linux systems including Ubuntu 18.04 LTS and Debian
 9.0 LTS, thus we only provide installation instructions for
 Debian/Ubuntu systems.
 
-##### 1\) Installing CGT dependencies
+#### 1\) Installing CGT dependencies
 
 Clone the repository locally <br/> `git clone
 https://github.com/hsmaan/CovidGenotyper`
@@ -149,15 +146,14 @@ library depdendencies - check Rscript output and install <br/>
     cd CovidGenotyper/bin
     Rscript --verbose packages_install.R
 
-##### 2\) Run preprocessing scripts
+#### 2\) Run preprocessing scripts
 
 CGT relies on pre-processing plot data prior to deployment to ensure
 visualizations can be loaded quickly. Fasta sequences should be
 downloaded from [GISAID’s EpiCoV database](https://www.gisaid.org/) and
 saved as `gisaid_cov2020_sequences_[mmm_dd].fasta` in the `data` folder.
-Metadata from [nextstrain’s ncov
-repository](https://github.com/nextstrain/ncov) should be saved as
-`gisaid_metadata_[mmm_dd].tsv`, also in the `data` folder.
+Metadata from GISAID should be saved as `gisaid_metadata_[mmm_dd].tsv`,
+also in the `data` folder.
 
 The order for processing scripts is the following:
 
@@ -168,7 +164,7 @@ The order for processing scripts is the following:
     Rscript --verbose maf_sites_out.R
     Rscript --verbose preprocess_plot_data.R
 
-##### 3\) Deploy CGT
+#### 3\) Deploy CGT
 
 Now that the shiny application dependencies have been installed and data
 has been preloaded, the shiny app can be deployed in a variety of ways,
@@ -212,6 +208,17 @@ following <br/>
   - ggplot2 v3.3.0
   - ggnetwork v0.5.8
   - plotly v4.9.2.1
+  - Cairo v1.5.11
+  - intergraph v2.0.2
+  - tidyverse v1.3.0
+  - data.table v1.12.8
+  - stringr v1.4.0
+  - reshape2 v1.4.3
+  - dplyr v0.8.5
+  - parallel v3.6.3
+  - ggthemes v4.2.0
+  - RColorBrewer v1.1.2
+  - GenomicRanges v1.38.0
 
 #### Command-line tools
 
@@ -221,9 +228,6 @@ following <br/>
 
 ## References
 
-  - Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C,
-    et al. NextStrain: Real-time tracking of pathogen evolution.
-    Bioinformatics. 2018;34(23):4121–3.
   - Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s
     innovative contribution to global health. Glob Challenges.
     2017;1(1):33–46.
@@ -266,6 +270,39 @@ following <br/>
   - Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et
     al. The variant call format and VCFtools. Bioinformatics.
     2011;27(15):2156–8.
+  - Simon Urbanek and Jeffrey Horner (2020). Cairo: R Graphics Device
+    using Cairo Graphics Library for Creating High-Quality Bitmap (PNG,
+    JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and
+    Win32) Output. R package version 1.5-11.
+    <https://CRAN.R-project.org/package=Cairo>
+  - Bojanowski, Michal (2015) intergraph: Coercion Routines for Network
+    Data Objects. R package version 2.0-2.
+    <http://mbojan.github.io/intergraph>
+  - Wickham et al., (2019). Welcome to the tidyverse. Journal of Open
+    Source Software, 4(43), 1686, <https://doi.org/10.21105/joss.01686>
+  - Matt Dowle and Arun Srinivasan (2019). data.table: Extension of
+    `data.frame`. R package version 1.12.8.
+    <https://CRAN.R-project.org/package=data.table>
+  - Hadley Wickham (2019). stringr: Simple, Consistent Wrappers for
+    Common String Operations. R package version 1.4.0.
+    <https://CRAN.R-project.org/package=stringr>
+  - Hadley Wickham (2007). Reshaping Data with the reshape Package.
+    Journal of Statistical Software, 21(12), 1-20. URL
+    <http://www.jstatsoft.org/v21/i12/>.
+  - Hadley Wickham, Romain François, Lionel Henry and Kirill Müller
+    (2020). dplyr: A Grammar of Data Manipulation. R package version
+    0.8.5. <https://CRAN.R-project.org/package=dplyr>
+  - R Core Team (2020). R: A language and environment for statistical
+    computing. R Foundation for Statistical Computing, Vienna, Austria.
+    URL <https://www.R-project.org/>.
+  - Jeffrey B. Arnold (2019). ggthemes: Extra Themes, Scales and Geoms
+    for ‘ggplot2’. R package version 4.2.0.
+    <https://CRAN.R-project.org/package=ggthemes>
+  - Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes. R package
+    version 1.1-2. <https://CRAN.R-project.org/package=RColorBrewer>
+  - Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, et al. (2013)
+    Software for Computing and Annotating Genomic Ranges. PLoS Comput
+    Biol 9(8): e1003118. <doi:10.1371/journal.pcbi.1003118>
 
 ## License
 
diff --git a/bin/gisaid_sequence_process.R b/bin/gisaid_sequence_process.R
@@ -2,7 +2,6 @@ library(ape)
 library(Biostrings)
 library(stringr)
 library(DECIPHER)
-library(stringi)
 library(data.table)
 library(tidyverse)
 
diff --git a/bin/maf_sites_out.R b/bin/maf_sites_out.R
@@ -3,7 +3,6 @@ library(tidyverse)
 library(Biostrings)
 library(ape)
 library(GenomicRanges)
-library(GenomicFeatures)
 library(stringr)
 
 # Load data
diff --git a/bin/packages_install.R b/bin/packages_install.R
@@ -7,7 +7,6 @@ install.packages("shinyWidgets")
 install.packages("Cairo")
 install.packages("intergraph")
 install.packages("tidyverse")
-install.packages("tidyverse")
 install.packages("data.table")
 install.packages("stringr")
 install.packages("reshape2")
@@ -19,11 +18,8 @@ install.packages("ggnetwork")
 install.packages("RColorBrewer")
 install.packages("uwot")
 install.packages("igraph")
-install.packages("stringi")
-install.packages("igraph")
 install.packages("ape")
 BiocManager::install("GenomicRanges")
-BiocManager::install("GenomicFeatures")
 BiocManager::install("Biostrings")
 BiocManager::install("DECIPHER")
 
