| grad_mplot {JMDplots} | R Documentation |
These are plotting functions for the redox gradients (gradox) and salinity gradients (gradH2O) papers.
The functions are exported in the package so they are available to user scripts.
mplot(study, seqtype, plottype = "bars", ylim = NULL, plot.RNA = TRUE,
taxid = NULL, dsDNA = TRUE, abbrev = NULL, col = NULL, add.label = TRUE,
maxdepth = NULL, H2O = FALSE, plot.it = TRUE, add.title = TRUE, yline = 2,
datadir = NULL, mdata = studies, add = FALSE,
pch = 19, var = NULL, srt = 45, ilabel = NULL)
mpage(subset = "gradoxSI", H2O = FALSE, plottype = "bars", dsDNA = TRUE,
set.par = TRUE, add.label = TRUE, mfrow = NULL)
ppage(subset = "gradoxSI", H2O = FALSE, set.par = TRUE, plot.it = TRUE,
add.label = TRUE, mfrow = NULL)
mcomp(mout, yvar = "RNA")
pcomp(mout, pout, seqtype = "MG", vars = NULL, parts = c("plot", "legend"),
yline = 2, xlim = NULL, ylim = NULL, reorder = TRUE,
plot.techtype = FALSE, add = FALSE, pch = NULL, lty = 2,
labels.at = "max", cex.ylab = 1, font = 1, labdx = NULL, labdy = NULL)
study |
character, name of study |
seqtype |
character, description of sequence data type |
plottype |
character, type of plot |
ylim |
numeric, y-axis limits |
plot.RNA |
logical, plot RNA compositions? |
taxid |
numeric, select only this taxid |
dsDNA |
logical, use chemical composition of double-stranded DNA? |
abbrev |
character, abbreviations for studies |
col |
character, line color |
add.label |
logical, label the plot with MG (metagenome) or MT (metatranscriptome)? |
maxdepth |
numeric, maximum sample depth (meters) |
H2O |
logical, plot nH2O instead of ZC? |
plot.it |
logical, make a plot (use FALSE to return processed data without plotting)? |
add.title |
logical, add a title to the plot? |
yline |
numeric, margin position for y-axis label |
var |
character, other variable to plot (‘GRAVY’ or ‘pI’) |
srt |
numeric, string rotation for non-numeric labels |
ilabel |
numeric, which labels to include on plot |
subset |
character, name of subset of studies to plot |
set.par |
logical, set up plot with |
mfrow |
numeric, optional setting for |
mout |
list, output from |
yvar |
character, y-axis variable (‘RNA’ or ‘GC’) |
pout |
list, output from |
vars |
character, variables to plot (‘ZC’, ‘H2O-ZC’, ‘GRAVY’, ‘pI’, or ‘pIG’) |
parts |
character, parts of figure to include |
xlim |
numeric, x-axis limits |
reorder |
logical, put points in order of increasing x value? |
plot.techtype |
logical, identify 454 or Sanger datasets by open symbols? |
add |
logical, add to existing plot? |
datadir |
character, location of data directory (default is from package) |
mdata |
list, metadata for studies (default is from package) |
pch |
numeric, plot symbol (default is determined from sample type) |
lty |
numeric, line type |
labels.at |
character, plot study labels at ‘max’ or ‘min’ values (use NA to omit labels) |
cex.ylab |
numeric, size of y-axis label |
font |
integer, font to use for study labels (see |
labdx |
numeric, x-adjustment for label position |
labdy |
numeric, y-adjustment for label position |
The study is composed of two names for the locality separated by an underscore.
For mplot, the seqtype contains the name of the database followed by an underscore and MG (metagenome) or MT (metatranscriptome), i.e. ‘[SRA|IMG|MGRAST|GenBank]_[MG|MT]’.
These can be changed to ‘_MGP’ and ‘_MTP’ to indicate protein sequences.
mplot plots a compositional variable for a particular combination of study and seqtype.
The variable plotted is ZC by default, but this can be changed to nH2O with H2O = TRUE or GRAVY or pI (specified in the var argument).
ZC of both DNA and RNA are plotted, with an offset of -0.28 applied to that of RNA, so that values can be shown on the same scale (see Dick et al., 2019).
The default value of plottype, ‘bars’, specifies a plot with mean values connected by dashed lines and error bars for each sample.
A polygon plot (shaded area instead of error bars) is made if the first character of plottype is ‘#’.
In this case, plottype is interpreted as the fill color for the polygon.
mcomp makes a scatterplot of (ZC of RNA - ZC of DNA) vs ZC of DNA.
Set yvar to ‘GC’ to change the y-axis to GC ratio of DNA.
(For double-stranded DNA, this should be a linear function of ZC.)
For pcomp, seqtype is just ‘MG’ or ‘MT’.
The variables (vars) are automatically determined based on the values of mout and pout.
Use vars = "GRAVY" or vars = "pI" to plot the values of GRAVY or pI instead of Zc.
Use vars = "pIG" to make a GRAVY-pI plot.
datadir and mdata are used to specify alternate location of compositional data and metadata for metagenomic studies.
This permits the processing of user-provided data sets; see subsurface for some examples.
Dick JM, Yu M, Tan J and Lu A (2019) Changes in carbon oxidation state of metagenomes along geochemical redox gradients. Front. Microbiol. 10, 120. doi:10.3389/fmicb.2019.00120
# plot ZC of DNA and RNA
mplot("Bison_Pool", "IMG_MG")
# plot ZC of protein
mplot("Bison_Pool", "IMG_MGP")
# make a page of plots of ZC of DNA and RNA
mout <- mpage()
# compare ZC of RNA and DNA for these datasets
mcomp(mout)
# compare GC and ZC of DNA for these datasets
mcomp(mout, yvar = "GC")
# make a page of plots of ZC of proteins
pout <- ppage()
# plot ZC of DNA vs proteins for the metagenomes
pcomp(mout, pout)
# plot ZC of DNA vs proteins for the metatranscriptomes
pcomp(mout, pout, "MT")
## TODO: plot nH2O of DNA vs proteins
#mout <- mpage(H2O = TRUE)
#pout <- ppage(H2O = TRUE)
#pcomp(mout, pout)
# plot nH2O vs ZC of proteins in a few redox gradients
mout <- ppage("gradoxGS")
pout <- ppage("gradoxGS", H2O = TRUE)
pcomp(mout, pout, reorder = FALSE, yline = 2)
# overlay data for protein from the Baltic Sea
mout <- ppage("balticsurface", plot.it = FALSE)
pout <- ppage("balticsurface", H2O = TRUE, plot.it = FALSE)
pcomp(mout, pout, reorder = FALSE, add = TRUE)
# plot nH2O vs GRAVY of proteins
pcomp(mout, pout, vars = "GRAVY")