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Replace plyr with tidyverse
Replace plyr::ldply calls
species should be species_name
The species name is recorded as $species_name in the input son, not $species. The latter used to work, probably due to partial matching, but doesn't always now. See line 118 here - https://github.com/caseywdunn/agalmar/blob/master/R/utility_functions.R
Warning - Found more than one class "DGEList" in cache
Sam Church noted the following, and I have seen it as well:
If you load agalmar first then you get a warning:
Found more than one class "DGEList" in cache; using the first, from namespace 'agalmar'
Where if you load edgeR first you still get a warning but it uses the namespace 'edgeR'. The problem is that some of the subsequent analyses I want to perform choke if DGEList comes from agalmar.
Here is the example line of code I want to apply - it corresponds to some of the code originally in the gene expression commands used with agalma, and the purpose is to process the json file and keep only the libraries for the desired treatments.
e <- mclapply(ag.data, Expression, mc.cores=1)
x <- e$whole_embryonic
y <- x@dge
treatments <- x@treatments
focal_treatments = c("Anterior_zero_two","Posterior_zero_two")
keep <- ( treatments %in% focal_treatments )
y <- y[,keep]
If DGEList comes from agalmar, then I get the error 'incorrect dimensions'
Add DESEQ2 in addition to edgeR
Create slots for both in Expression object, and populate on data load
add more nhx tests
Add more tests to evaluate successful parsing of nhx fields and their addition to the nhx@phylo tree.
Create summary stats for references and expression libraries
Change existing summary_frame to summarize_libraries method.
Create new summarize_reference method that provides details on the number of reference genes by protein coding, rRNA, etc.
Create function summary_libraries based on existing manuscript code that creates a summary data frame of stats for each expression library in a list of Expression objects.
Create function summary_references that creates a summary data frame of reference stats from a list of Expression objects.
Move DESeq2 analysis out of `Expression()`
At present the DESeq2::DESeqDataSetFromMatrix() constructor call is in the agalmar Expression() constructor. Unlike edgeR, the DESeq2 constructor runs the analysis given a particular model.
Move DESeq2::DESeqDataSetFromMatrix() to a separate method that returns a DESeq2 object given a specified model. Call the new method create_DESeq2(design)
ERROR: dependency ‘treeio’ is not available for package ‘agalmar’
Hi! Not really an issue because I was able to fix, so feel free to close. Wanted to share here in case it helps anyone. Looking forward to exploring functions in this package. Thank you!
Installing in RStudio (MacOS 10_13_3, RStudio 1.1.383, R 3.4.2) with:
install_github('caseywdunn/agalmar')
Fixed with this from recommendation:
install.packages("base64enc", type = "binary")
install.packages("jsonlite", type="binary")
install.packages("rmarkdown")
devtools::install_github("tidyverse/reprex")
source("https://bioconductor.org/biocLite.R")
biocLite("treeio")
install_github('caseywdunn/agalmar')
Error messages:
> install_github('caseywdunn/agalmar')
Downloading GitHub repo caseywdunn/agalmar@master
from URL https://api.github.com/repos/caseywdunn/agalmar/zipball/master
Installing agalmar
Downloading GitHub repo caseywdunn/hutan@master
from URL https://api.github.com/repos/caseywdunn/hutan/zipball/master
Installing hutan
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore \
--quiet CMD INSTALL \
'/private/var/folders/5m/37fhf86x0g70t9w632_f9yf80000gn/T/RtmpCHxgE5/devtools875e654ab908/caseywdunn-hutan-ff536f3' \
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests
* installing *source* package ‘hutan’ ...
Warning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'zone/tz/2018c.1.0/zoneinfo/America/Los_Angeles'
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hutan)
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore \
--quiet CMD INSTALL \
'/private/var/folders/5m/37fhf86x0g70t9w632_f9yf80000gn/T/RtmpCHxgE5/devtools875e4bfb0cb8/caseywdunn-agalmar-33d5a33' \
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests
ERROR: dependency ‘treeio’ is not available for package ‘agalmar’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/agalmar’
Installation failed: Command failed (1)
Tried biocLite("treeio") with the following error:
ERROR: dependency ‘rmarkdown’ is not available for package ‘reprex’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/reprex’
The downloaded source packages are in
‘/private/var/folders/5m/37fhf86x0g70t9w632_f9yf80000gn/T/RtmpCHxgE5/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘reprex’ had non-zero exit status
Tried install.packages("reprex") with the following error:
ERROR: dependency ‘rmarkdown’ is not available for package ‘reprex’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/reprex’
Warning in install.packages :
installation of package ‘reprex’ had non-zero exit status
Update expression to match output from Agalma v 1.0.1
The newest version of Agalma includes fpkm and gene length outputs that need to be parsed - add lengths, fpkm to setClass and to the function
Parse nhx trees
At present gene trees are only parsed in newick format. Parse in nhx format to preserve information on duplications etc.
A few packages do this, including ggtree: https://bioconductor.org/packages/release/bioc/vignettes/ggtree/inst/doc/treeImport.html#parsing-nhx-tree
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