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R package for downstream analysis for anacapa eDNA pipeline

Home Page: https://f1000research.com/articles/7-1734/v1

License: GNU General Public License v3.0

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natetruelove yvanlebras flefa caledna erifa1 kballare levisimons hobbeist

ranacapa's Issues

Do things with continuous metadata?

We currently don't do anything with continuous metadata (everything gets treated as categorical- or there's just no test run). It might be worth doing a few simple things with continuous variables (scatterplot of diversity by variable, scatterplot of NMDS distance vs. Euclidean distance of variable)

bigger rarefaction plots

the facet_wrap()'ed plots on the rarefaction page are quite small as @madcowen pointed out. Will think of alternatives- perhaps just no faceting

Organize the app into "modules" so that the info is not all written in ui.R

https://shiny.rstudio.com/articles/modules.html; see also ShinyDiversity's repo

Error running runRanacapa()

Hi I get this error running runRanacapa(). Any ideas what I can try?

> runRanacapaApp()

Listening on http://127.0.0.1:4899
Warning: Error in .Call: Incorrect number of arguments (6), expecting 4 for 'unserialize_from_yaml'
  67: yaml.load
  66: yaml::yaml.load_file
  65: getDependency
  64: widget_dependencies
  63: htmlwidgets::shinyWidgetOutput
  61: DT::dataTableOutput
Warning: Error in .Call: Incorrect number of arguments (6), expecting 4 for 'unserialize_from_yaml'
  67: yaml.load
  66: yaml::yaml.load_file
  65: getDependency
  64: widget_dependencies
  63: htmlwidgets::shinyWidgetOutput
  61: DT::dataTableOutput

> session_info()
- Session info --------------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.2 (2016-10-31)
 os       Windows >= 8 x64            
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United Kingdom.1252 
 ctype    English_United Kingdom.1252 
 tz       Europe/London               
 date     2018-11-16                  

- Packages ------------------------------------------------------------------------------------------------------------------------------------------
 package         * version date       lib source                            
 ade4              1.7-13  2018-08-31 [1] CRAN (R 3.3.2)                    
 ape               5.2     2018-09-24 [1] CRAN (R 3.3.2)                    
 assertthat        0.2.0   2017-04-11 [1] CRAN (R 3.3.3)                    
 backports         1.1.2   2017-12-13 [1] CRAN (R 3.3.3)                    
 base64enc         0.1-3   2015-07-28 [1] CRAN (R 3.3.2)                    
 bindr             0.1.1   2018-03-13 [1] CRAN (R 3.3.3)                    
 bindrcpp        * 0.2.2   2018-03-29 [1] CRAN (R 3.3.3)                    
 Biobase           2.34.0  2016-10-18 [1] Bioconductor                      
 BiocGenerics      0.20.0  2016-10-18 [1] Bioconductor                      
 biomformat        1.2.0   2016-10-18 [1] Bioconductor                      
 Biostrings        2.42.1  2016-12-01 [1] Bioconductor                      
 callr             3.0.0   2018-08-24 [1] CRAN (R 3.3.2)                    
 cli               1.0.1   2018-09-25 [1] CRAN (R 3.3.2)                    
 cluster           2.0.5   2016-10-08 [2] CRAN (R 3.3.2)                    
 codetools         0.2-15  2016-10-05 [2] CRAN (R 3.3.2)                    
 colorspace        1.3-2   2016-12-14 [1] CRAN (R 3.3.2)                    
 crayon            1.3.4   2017-09-16 [1] CRAN (R 3.3.3)                    
 crosstalk         1.0.0   2016-12-21 [1] CRAN (R 3.3.3)                    
 curl              3.2     2018-03-28 [1] CRAN (R 3.3.3)                    
 data.table      * 1.11.8  2018-09-30 [1] CRAN (R 3.3.2)                    
 desc              1.2.0   2018-05-01 [1] CRAN (R 3.3.2)                    
 devtools        * 2.0.1   2018-10-26 [1] CRAN (R 3.3.2)                    
 digest            0.6.18  2018-10-10 [1] CRAN (R 3.3.2)                    
 dplyr           * 0.7.4   2017-09-28 [1] CRAN (R 3.3.3)                    
 DT                0.5     2018-11-05 [1] CRAN (R 3.3.2)                    
 foreach           1.4.4   2017-12-12 [1] CRAN (R 3.3.3)                    
 fs                1.2.6   2018-08-23 [1] CRAN (R 3.3.2)                    
 ggplot2         * 2.2.1   2016-12-30 [1] CRAN (R 3.3.2)                    
 glue              1.3.0   2018-07-17 [1] CRAN (R 3.3.2)                    
 gtable            0.2.0   2016-02-26 [1] CRAN (R 3.3.2)                    
 htmltools         0.3.6   2017-04-28 [1] CRAN (R 3.3.3)                    
 htmlwidgets       1.3     2018-09-30 [1] CRAN (R 3.3.2)                    
 httpuv            1.4.5   2018-07-19 [1] CRAN (R 3.3.2)                    
 httr              1.3.1   2017-08-20 [1] CRAN (R 3.3.3)                    
 igraph            1.1.2   2017-07-21 [1] CRAN (R 3.3.3)                    
 IRanges           2.8.2   2017-03-18 [1] Bioconductor                      
 iterators         1.0.10  2018-07-13 [1] CRAN (R 3.3.2)                    
 jsonlite          1.5     2017-06-01 [1] CRAN (R 3.3.3)                    
 later             0.7.5   2018-09-18 [1] CRAN (R 3.3.2)                    
 lattice           0.20-34 2016-09-06 [2] CRAN (R 3.3.2)                    
 lazyeval          0.2.1   2017-10-29 [1] CRAN (R 3.3.3)                    
 magrittr          1.5     2014-11-22 [1] CRAN (R 3.3.2)                    
 markdown          0.8     2017-04-20 [1] CRAN (R 3.3.3)                    
 MASS              7.3-45  2016-04-21 [2] CRAN (R 3.3.2)                    
 Matrix            1.2-7.1 2016-09-01 [2] CRAN (R 3.3.2)                    
 memoise           1.1.0   2017-04-21 [1] CRAN (R 3.3.3)                    
 mgcv              1.8-15  2016-09-14 [2] CRAN (R 3.3.2)                    
 mime              0.6     2018-10-05 [1] CRAN (R 3.3.2)                    
 multtest          2.30.0  2016-10-18 [1] Bioconductor                      
 munsell           0.5.0   2018-06-12 [1] CRAN (R 3.3.2)                    
 nlme              3.1-128 2016-05-10 [2] CRAN (R 3.3.2)                    
 permute           0.9-4   2016-09-09 [1] CRAN (R 3.3.2)                    
 phyloseq        * 1.19.1  2016-12-30 [1] Bioconductor                      
 pillar            1.1.0   2018-01-14 [1] CRAN (R 3.3.3)                    
 pkgbuild          1.0.2   2018-10-16 [1] CRAN (R 3.3.2)                    
 pkgconfig         2.0.2   2018-08-16 [1] CRAN (R 3.3.2)                    
 pkgload           1.0.1   2018-10-11 [1] CRAN (R 3.3.2)                    
 plotly          * 4.7.1   2017-07-29 [1] CRAN (R 3.3.3)                    
 plyr              1.8.4   2016-06-08 [1] CRAN (R 3.3.3)                    
 prettyunits       1.0.2   2015-07-13 [1] CRAN (R 3.3.3)                    
 processx          3.2.0   2018-08-16 [1] CRAN (R 3.3.2)                    
 promises          1.0.1   2018-04-13 [1] CRAN (R 3.3.3)                    
 ps                1.2.0   2018-10-16 [1] CRAN (R 3.3.2)                    
 purrr             0.2.5   2018-05-29 [1] CRAN (R 3.3.2)                    
 R6                2.3.0   2018-10-04 [1] CRAN (R 3.3.2)                    
 ranacapa        * 0.1.0   2018-11-08 [1] Github (gauravsk/ranacapa@09cdc27)
 Rcpp              0.12.19 2018-10-01 [1] CRAN (R 3.3.2)                    
 remotes           2.0.1   2018-10-19 [1] CRAN (R 3.3.2)                    
 reshape         * 0.8.8   2018-10-23 [1] CRAN (R 3.3.2)                    
 reshape2          1.4.3   2017-12-11 [1] CRAN (R 3.3.3)                    
 rhdf5             2.18.0  2016-10-18 [1] Bioconductor                      
 rlang             0.2.0   2018-02-20 [1] CRAN (R 3.3.3)                    
 rprojroot         1.3-2   2018-01-03 [1] CRAN (R 3.3.3)                    
 rsconnect         0.8.8   2018-03-09 [1] CRAN (R 3.3.3)                    
 rstudioapi        0.8     2018-10-02 [1] CRAN (R 3.3.2)                    
 S4Vectors         0.12.2  2017-03-18 [1] Bioconductor                      
 scales            1.0.0   2018-08-09 [1] CRAN (R 3.3.2)                    
 sessioninfo       1.1.0   2018-09-25 [1] CRAN (R 3.3.2)                    
 shiny           * 1.1.0   2018-05-17 [1] CRAN (R 3.3.2)                    
 shinythemes     * 1.1.2   2018-11-06 [1] CRAN (R 3.3.2)                    
 splitstackshape * 1.4.6   2018-07-23 [1] CRAN (R 3.3.2)                    
 stringi           1.1.6   2017-11-17 [1] CRAN (R 3.3.3)                    
 stringr         * 1.2.0   2017-02-18 [1] CRAN (R 3.3.3)                    
 survival          2.42-6  2018-07-13 [1] CRAN (R 3.3.2)                    
 testthat          2.0.1   2018-10-13 [1] CRAN (R 3.3.2)                    
 tibble            1.4.2   2018-01-22 [1] CRAN (R 3.3.3)                    
 tidyr           * 0.8.1   2018-05-18 [1] CRAN (R 3.3.2)                    
 tidyselect        0.2.3   2017-11-06 [1] CRAN (R 3.3.3)                    
 usethis         * 1.4.0   2018-08-14 [1] CRAN (R 3.3.2)                    
 vegan             2.5-3   2018-10-25 [1] CRAN (R 3.3.2)                    
 viridisLite       0.3.0   2018-02-01 [1] CRAN (R 3.3.3)                    
 withr             2.1.2   2018-03-15 [1] CRAN (R 3.3.3)                    
 xtable            1.8-3   2018-08-29 [1] CRAN (R 3.3.2)                    
 XVector           0.14.1  2017-03-18 [1] Bioconductor                      
 yaml            * 2.2.0   2018-07-25 [1] CRAN (R 3.3.2)                    
 zlibbioc          1.20.0  2016-10-18 [1] Bioconductor                      

[1] C:/Users/basti/Documents/R/win-library/3.3
[2] C:/Program Files/R/R-3.3.2/library

Add Markdown to DESCRIPTION

I think recent updates have made it so that we need to add the markdown package to the DESCRIPTION file.

small app edits

I think it would be helpful to have a short description of what the demo dataset is if users select "demo" @gauravsk
rotating axes in alpha diversity plot didn’t give x axis enough space! same with taxonomy barplot. make margin a little bigger
PCoA make title of plot fully capitalized (Dissimilarity Method)
In Beta div stats tab, explain “Adonis”? Or don't call the tables Adonis and Pairwise adonis. @gauravsk
(small annoying thing—the genus and species levels of taxonomy barplot take a LONG time and clicking to other tabs doesn’t stop this :( wonder if there should be a pause button or something?) note that i wasn’t patient enough to even see if genus or species worked for unrarefied, beecause it took a long time, and got a warning to use devtools::install_github('hadley/ggplot2') for ggplotly. Maybe subset this demo dataset?? the taxonomy heat map also takes a fairly long time and that would be better with a subset of the demo dataset, too, but it's a reasonable amount of time.

beta diversity functionality temporarily broken- workaround in here

I got an email from the MIMG109 folks saying that their students were running into errors with the beta diversity tab of the ranacapa app on some computers, but not on others:

I figured out that the computers having this issue were running vegan v 2.5-1, whereas those that were not having this issue were running vegan v 2.4-6. The issue comes up because of recent updates to vegan that have not yet made their way into phyloseq. Some ongoing discussion about similar errors here.

The temporary workaround for this is to roll back to vegan v 2.4.-6, which can be done with the following steps:


remove.packages("vegan")
remove.packages("phyloseq")
remove.packages("ranacapa")

devtools::install_version("vegan", version = "2.4-6", repos = "http://cran.us.r-project.org")
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")
# IMPORTANT! When asked if you want to update packages, including Vegan, enter 'n'
devtools::install_github("gauravsk/ranacapa")

It might be worth redoing how we manage package imports

Hadley Wickham suggests using the package::function() syntax when writing code:

Adding a package dependency here ensures that it’ll be installed. However, it does not mean that it will be attached along with your package (i.e., library(x)). The best practice is to explicitly refer to external functions using the syntax package::function(). This makes it very easy to identify which functions live outside of your package. This is especially useful when you read your code in the future.

If you use a lot of functions from other packages this is rather verbose. There’s also a minor performance penalty associated with :: (on the order of 5µs, so it will only matter if you call the function millions of times). You’ll learn about alternative ways to call functions in other packages in namespace imports.

Some more info about this here

It probably doesn't matter a whole lot, but might be worth it to make code more readable I guess

download rarefied files

@limey-bean suggested adding a download button for rarefied files

ggrare_grouping samples

Out of curiosity, is it possible to include an argument to group the samples based on metadata while plotting the rarefaction curve?
For instace, ggrare(gp, step = 1000, color = "SampleType", label = "Sample", group = "habitat", se = T)

Thanks

test not working

Hi Gaurav, recently ranacapa as an R package stopped working for me. The Shiny app still works fine.
If I run the test, I get:

── Error (Line 4): conversion to physeq object works for good files ─────────────────────
Error: .data must be a data frame without row names.
Backtrace:

testthat::expect_is(...)
tibble::column_to_rownames(., "sum.taxonomy")

And later I get:
── Error (Line 3): duplicate entries in taxon table get summarized ─────────────────────
Error: error in evaluating the argument 'x' in selecting a method for function 'nrow': error in evaluating the argument 'object' in selecting a method for function 'tax_table': .data must be a data frame without row names.
Backtrace:

testthat::expect_equal(...)
base::.handleSimpleError(...)
base:::h(simpleError(msg, call))
Error (Line 2): extra entries in metadata file get filtered out ─────────────────────
Error: error in evaluating the argument 'x' in selecting a method for function 'nrow': error in evaluating the argument 'object' in selecting a method for function 'sample_data': .data must be a data frame without row names.
Backtrace:
testthat::expect_equal(...)
base::.handleSimpleError(...)
base:::h(simpleError(msg, call))

Any advice?

Thank you so much.

refer to external functions using 'packagename::function()'

On running devtools::check() I of course get a ton of messages that look like

convert_anacapa_to_phyloseq: no visible global function definition for
  ‘column_to_rownames’

The recommended workflow here is to explicitly state packagename in front of external function names, e.g. here the function should read tibble::column_to_rownames(...)

switch to using read_delim everywhere

use read delim and maybe pipe it to a data.frame() to maintain downstream functionality

ranacapa_automated.R file link is broken

Hello,
The link to the ranacapa_automated.R file is a 404 dead end. Is there another way to get the R script to run rANACAPA locally instead of through the shiny app? I'm having trouble uploading my input files to the shiny app (it says file size limit exceeded), so I thought I would try running it on my machine...
Thanks so much!

allow the use of the rarefied tables for barplot/heatmap

Right now the heatmap and the barplot are made on unrarefied samples. Give users the option to choose which one the plot should be made from.

how to draw a line?

Hello
tried abline function and geom_hline function to draw a line but didn't work.
any suggestion?

p <- ggrare(ps.3, step = 1000, color = "treatment", 
       label = rownames(sample_data(ps.3)),
       parallel = TRUE, # parallel is to make the process faster 
       se = FALSE) +
  facet_wrap(~treatment) +
  labs(x = "Sample Size", y = "Observed ASVs")
trail one 
p + abline(v= quantile(sample_sums(ps.prev@otu_table), 0.25)) 
trail two 
p + abline(v= 2476) # draw a vertical line at the min of the sample sums
trail three 
p +  geom_hline(xintercept = 2476, color = "red")

Thanks

Maximum upload size exceeded

When I upload a biom file (size:16 Mb). it show this error: Maximum upload size exceeded
How to fix it ?

laundry list of things to be fixed

Overall

there's a bunch of places where the spacing isn't great in the app (e.g. axis labels get cut off)- could probably just make the plots smaller

On alpha diversity page

Give users option to rotate the axis labels
Right now, on the alpha diversity plots, if the samples are grouped by a variable (e.g. depth), and a user hovers over a point, the value of the point is shown but not the identity of the point. This makes it hard to figure out, e.g. "which of the low depth plots has the highest sp richness". Can we figure out a way that hovering over a point shows the sample name of the point?

On beta diversity page

in server.R, get rid of the "big old heat map" lines
in server.R, get rid of the "network map" lines
also get rid of the two above from the call to grid.arrange
uncomment lines in ui.R so that the ward linkage map does get shown

Taxonomy barplot

I think the barplot doesnt use theme_ranacapa right now- has a gray background.

Taxonomy heat map

No scale bar generated- can we add one

some useful info for app deployment

Using this issue to keep track of things that help during app deployment.

options(repos = BiocInstaller::biocinstallRepos())

helps with bioconductor packages

Barplots size and other suggestions for improvements

Hi,

thank you for this really great app, with some minor manipulation of standard formats it's really able to give a quick and awesome glimpse of data. I have just a couple of small questions/enhancement requests:

Plots like "taxonomy barplot" would look better if it would be possible to adjust the axis sizes, especially the y-axis when there are a lot of OTUs/ASVs. And this is related to the second question:
Still in the taxonomy barplot, it would be nice to have the option to display the top Ns taxa based eg on the sum of the abundance across samples (I know there is plenty of ways to select the top Ns taxa, this is just my favourite one :D). I guess I could subset the taxa before importing the data into the app, but this would screw with the other statistics.

My guess is that these enhancements are not very hard to implement, but my skills with shinyapps are not this extended :D

Again, this is a great app! I hope you're still developing and taking care of it.

Domenici

"continuous variable cannot be mapped to shape"

the error above shows up for Maddi on the alpha div plots- figure out what's causing and fix ths

Rename runExample

It's a silly name!

Give people the option to treat continuous variable as categorical, don't force it

Sometimes a metadata column may be numeric but actually be categorical, e.g. Replicate number. I think the right thing to do will be to add options on the front/landing page for people to declare variables as continuous or categorical

remove taxonomy paths with 0 occurrences from taxon table

I think this can be done in the convert_anacapa_to_physeq function

Error in seq.default(1, tot[i], by = step) : wrong sign in 'by' argument

When I try to run the ggrare function on my phyloseq object, I get the following error: Error in seq.default(1, tot[i], by = step) : wrong sign in 'by' argument.

Any clue what this means or what might be causing it? I tried setting step to many different values (1,10,100,1000) as well as deleting it entirely from the code but nothing changed the error I got.

taxonomy barplot categories

figure out why there are different sections in a given barplot in the taxonomy barplot tab of the shiny app for the same phylum, class, etc.

include decontamination capability

check if this is an issue in the app

From Sabrina:

Hey! so this may have been fixed already ( i cant tell because I dont see a scripted version of ranacapa on your or the anacapa github)…. the one that I have has a small bug in the beta diversity calculations…. it does not recalculate the distance matrix when switching to the bray method of analysis…. it was an easy fix by just adding

d <- distance(physeq_obj_rare, method=dissimMethod)
sampledf <- data.frame(sample_data(physeq_obj_rare))
veganComm <- vegan_otu(physeq_obj_rare)
ord <- ordinate(physeq_obj_rare, method = "MDS", distance = d)

after

dissimMethod = "bray"

so it was using the jaccard distance matrix for both the bray and jaccard analyses and therefore giving the same results for both

Turn off legend on rarefaction plots in `ranacapa-automated`

Rarefaction plot made from the automated pipeline looks like this right now:

rarefaction_output.pdf

Just turn off the legend, it's unhelpful for large number of samples anyway