Gapminder links:
http://staff.math.su.se/hoehle/blog/2018/07/02/factfulness.html
and raw content:
https://raw.githubusercontent.com/hoehleatsu/hoehleatsu.github.io/master/_source/2018-07-02-factfulness.Rmd
http://rstudio-pubs-static.s3.amazonaws.com/116038_0ebe7e3db5dd4f29ac10e0c994373f99.html
http://stat545.com/block019_enforce-color-scheme.html#circle-area-population
dplyr
https://dplyr.tidyverse.org/articles/programming.html
https://datacarpentry.org/R-ecology-lesson/03-dplyr.html
http://stat545.com/bit001_dplyr-cheatsheet.html
https://cran.r-project.org/web/packages/tibble/vignettes/tibble.html
http://www.sthda.com/english/wiki/ggplot2-box-plot-quick-start-guide-r-software-and-data-visualization
http://r4ds.had.co.nz/
Friday, 17 August 2018
Friday, 6 July 2018
Making changes online on Overleaf...
I needed to learn some Latex.
Here is some info about captions - i.e. a figure legends:
https://tex.stackexchange.com/questions/268554/how-to-put-a-legend-under-a-figure
https://www.overleaf.com/help/52-how-do-i-insert-an-image-at-a-specific-point-in-the-document#.Wz9ALxJKhR0
https://www.overleaf.com/17638816rrfvjhxbxqjh#/66943761/
https://www.sharelatex.com/project/515c83650651e57e1975aeb2
Here is the way to have bold and normal text in the caption:
https://tex.stackexchange.com/questions/3276/caption-is-bold-can-i-have-part-of-it-not-bold
Lots about captions here:
http://www.ctex.org/documents/packages/float/caption.pdf
FINAL point:
Making a DOI for my code:
https://guides.github.com/activities/citable-code/
Here is some info about captions - i.e. a figure legends:
https://tex.stackexchange.com/questions/268554/how-to-put-a-legend-under-a-figure
https://www.overleaf.com/help/52-how-do-i-insert-an-image-at-a-specific-point-in-the-document#.Wz9ALxJKhR0
https://www.overleaf.com/17638816rrfvjhxbxqjh#/66943761/
https://www.sharelatex.com/project/515c83650651e57e1975aeb2
Here is the way to have bold and normal text in the caption:
https://tex.stackexchange.com/questions/3276/caption-is-bold-can-i-have-part-of-it-not-bold
Lots about captions here:
http://www.ctex.org/documents/packages/float/caption.pdf
FINAL point:
Making a DOI for my code:
https://guides.github.com/activities/citable-code/
Wednesday, 13 June 2018
Trying to test drawProteins with new version of ggplot2...
A new version of ggplot2 is being launched.
I need to check this with my package drawProteins.
Here is the information about the new version of ggplot2:
https://github.com/tidyverse/ggplot2/blob/master/NEWS.md#ggplot2-2219000
Here is a link about how to a development version of ggplot2:
https://gist.github.com/kohske/1150934
Step 1: Create new Project in RStudio
Step 2: The script:
# script to test drawProteins with new version of ggplot2
# install devtools
install.packages('devtools')
# install dependency of scales package
install.packages(c("RColorBrewer", "stringr", "dichromat", "munsell", "plyr", "colorspace"))
install.packages("Rcpp")
# install dependency of ggplot2 package
install.packages("rlang")
# Open devtools package
library(devtools)
# move to development mode
# scales and ggplot2 are installed in "~/R-dev" directory, so official version of ggplot2 are not removed.
dev_mode(TRUE)
# download development version of scales and ggplot2
install_github("hadley/scales", force=TRUE)
# main branch of development
install_github("hadley/ggplot2")
# (Optional) install_github("ggplot2", "kohske", "feature/new-guides-with-gtable")
# activate development version of ggplot2
library(ggplot2)
# install bioconductor version of drawProteins
source("https://bioconductor.org/biocLite.R")
biocLite("drawProteins")
library(drawProteins)
source("https://bioconductor.org/biocLite.R")
biocLite("BiocStyle")
# run some tests...
# try to compile vignette
# vignette seems to assembled OK....
Comments
Interestingly we now have a d> cursor...
Needed to download version 3.5 of R.
Then need lots of new installs....
Needed a new version of Rccp and rlang packages as well.
html of vignette seems like an easy way to test.
All looks good...
Figures assembled without errors.
Session info:
Says drawProteins_1.0.0
and
ggplot2_2.2.1.9000
so new version.
Basically this implies that these two should work together OK.
Good news.
I need to check this with my package drawProteins.
Here is the information about the new version of ggplot2:
https://github.com/tidyverse/ggplot2/blob/master/NEWS.md#ggplot2-2219000
Here is a link about how to a development version of ggplot2:
https://gist.github.com/kohske/1150934
Step 1: Create new Project in RStudio
Step 2: The script:
# script to test drawProteins with new version of ggplot2
# install devtools
install.packages('devtools')
# install dependency of scales package
install.packages(c("RColorBrewer", "stringr", "dichromat", "munsell", "plyr", "colorspace"))
install.packages("Rcpp")
# install dependency of ggplot2 package
install.packages("rlang")
# Open devtools package
library(devtools)
# move to development mode
# scales and ggplot2 are installed in "~/R-dev" directory, so official version of ggplot2 are not removed.
dev_mode(TRUE)
# download development version of scales and ggplot2
install_github("hadley/scales", force=TRUE)
# main branch of development
install_github("hadley/ggplot2")
# (Optional) install_github("ggplot2", "kohske", "feature/new-guides-with-gtable")
# activate development version of ggplot2
library(ggplot2)
# install bioconductor version of drawProteins
source("https://bioconductor.org/biocLite.R")
biocLite("drawProteins")
library(drawProteins)
source("https://bioconductor.org/biocLite.R")
biocLite("BiocStyle")
# run some tests...
# try to compile vignette
# vignette seems to assembled OK....
Interestingly we now have a d> cursor...
Needed to download version 3.5 of R.
Then need lots of new installs....
Needed a new version of Rccp and rlang packages as well.
html of vignette seems like an easy way to test.
All looks good...
Figures assembled without errors.
Session info:
Says drawProteins_1.0.0
and
ggplot2_2.2.1.9000
so new version.
Basically this implies that these two should work together OK.
Good news.
Monday, 9 April 2018
Some MAP kinase links...
I want to prepare a visualisation of MAP Kinase proteins in different species:
- probably fly, chicken, mouse and human as a starting point.
Search reveals these sources:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026999
- probably fly, chicken, mouse and human as a starting point.
Search reveals these sources:
- Evolutionary History of the Vertebrate Mitogen Activated Protein Kinases Family
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026999
- Evolutionary history of mitogen-activated protein kinase (MAPK) genes in Lotus, Medicago, and Phaseolus
these are plants - soya bean.
https://www.tandfonline.com/doi/full/10.4161/psb.27189- Wikipathways - chicken https://www.wikipathways.org/index.php/Pathway:WP769
- Interpro: https://www.ebi.ac.uk/interpro/entry/IPR003527
UniProt search:
family:"protein kinase superfamily cmgc ser thr protein kinase family map kinase subfamily" AND organism:"Gallus gallus (Chicken) [9031]"
API Queries for UniProt
Uniprot search for:
protein kinase superfamily cmgc ser thr protein kinase family map kinase subfamily
Gives 205 protein entries across various species.
Go Ontology
F1000 Bioconductor Gateway
New article describing the tool, I used:
https://f1000research.com/articles/7-431/v1?utm_medium=email&utm_source=tracked_articles_alert
Authoring Bioconductor workflows with BiocWorkflowTools [version 1; referees: awaiting peer review]
https://f1000research.com/articles/7-431/v1?utm_medium=email&utm_source=tracked_articles_alert
Authoring Bioconductor workflows with BiocWorkflowTools [version 1; referees: awaiting peer review]
Animal pics - Phylopic...
A search revealed this StackOverflow post:
https://stackoverflow.com/questions/28206611/adding-custom-image-to-geom-polygon-fill-in-ggplot
which led to rphylopic (https://github.com/sckott/rphylopic)
which seems interesting and relevant.
Link here to the parent site: http://phylopic.org/about/
https://stackoverflow.com/questions/28206611/adding-custom-image-to-geom-polygon-fill-in-ggplot
which led to rphylopic (https://github.com/sckott/rphylopic)
which seems interesting and relevant.
Link here to the parent site: http://phylopic.org/about/
Friday, 6 April 2018
Grappling with writing a paper in RMarkdown...
I have submitted a manuscript to F1000Research as part of the Bioconductor Gateway. It's about drawProteins.
The workflow involved:
A busy day of work...
Here are a few of the resources I used to help write the manuscript:
The workflow involved:
- Writing text and code in RMarkdown using R Studio
- Using BiocWorkflowTools (https://www.bioconductor.org/packages/release/bioc/html/BiocWorkflowTools.html)
- Putting in citations from Bibdesk
- Knitting with knitr in R Studio which creates multiple files...
- A PDF
- A tex file
- A folder of latex figures (names not ideal, I think).
- Uploading files to Overleaf
- Logging into F1000Research
- Linking into Overleaf
- The uploading a Word file too (separate Rmd file and Knit required and some manual editing - WHY?)
- Adding cover letter
- Identifying referees - finding emails can be difficult!
A busy day of work...
Here are a few of the resources I used to help write the manuscript:
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