User-provided data for metagenomes

Description

Metadata for two subsurface metagenomes, used as an example of user-provided data.

Details

To use user-provided data, do one of the following: Call ppage with an argument for subset that is a list with the metadata, and have the CSV files of DNA, RNA, or protein composition under the data directory of the working directory. Or, call mplot with the path of the data directory given in datadir.

For the example here, the extdata/subsurface/data directory has additional files of amino acid compositions for two subsurface environments: North Pond metagenome (Tully et al., 2018) and Peru Margin metatranscriptome (Orsi et al., 2013).

References

Orsi WD, Edgcomb VP, Christman GD and Biddle JF (2013) Gene expression in the deep biosphere. Nature 499, 205-208. doi:10.1038/nature12230

Tully BJ, Wheat CG, Glazer BT and Huber JA (2018) A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer ISME J. 12, 1-16. doi:10.1038/ismej.2017.187

Examples

# create the metadata
subsurface <- list(
  Peru_Margin = list( # 20180313 [OECB13]
    depth = c("5m", "30m", "50m", "70m", "91m", "159m"),
    SRA_MT = c("SRX187180","SRX330851","SRX331883","SRX331884","SRX331956","SRX331958"),
    MT_range = c(1.64, 1.72),
    MTP_range = c(-0.18, -0.13),
    abbrev = "PM",
    group = "rock",
    plot_real_x = FALSE
  ),
  North_Pond = list( # 20180320 [TWGH18]
    # time points of samples from U1832A 
    sample = c("TP1", "TP2", "TP3", "TP4", "TP5", "TP6", "TP7", "TP8", "TP9", "CTD"),
    SRA_MG = c("SRX3143893", "SRX3143894", "SRX3143895", "SRX3143896", "SRX3143897",
               "SRX3143898", "SRX3143899", "SRX3143900", "SRX3143886", "SRX3143890"),
    MG_range = c(1.63, 1.71),
    MGP_range = c(-0.18, -0.14),
    abbrev = "NP",
    group = c("oxygenated", "oxygenated", "oxygenated", "oxygenated", "oxygenated",
              "oxygenated", "oxygenated", "oxygenated", "oxygenated", "oxygenated0"),
    plot_real_x = FALSE
  )
)

# make plot for one data set
datadir <- system.file("extdata/subsurface/data", package = "JMDplots")
mplot("North_Pond", "SRA_MGP", datadir = datadir, mdata = subsurface)

# make plots for multiple data sets
WD <- setwd(system.file("extdata/subsurface", package = "JMDplots"))
ppage(subsurface)
setwd(WD)