Description Usage Arguments Value Examples
View source: R/plotting-functions.R
Plots EICs from ion mode duplicates using
plotEICs-methods
from CAMERA
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | plot_ionduplicate(
anposGa,
xpos,
annegGa,
xneg,
rt.method,
Peak.list,
gen.plots,
file.base,
QC.id,
mytable,
maxEIC,
maxQC,
...
)
|
anposGa |
|
xpos |
|
annegGa |
|
xneg |
|
rt.method |
Which method to use for EIC. Can be one of
|
Peak.list |
data.frame containing combined ion mode peaklist with column
|
gen.plots |
logical indicating whether to create plots for ion mode
duplicates. Default is |
file.base |
character string used to name graphical output. Default is
|
QC.id |
character identifier for pooled QC samples. Default is
|
mytable |
character name of table in database to return |
maxEIC |
numeric Max number of features for which to |
maxQC |
numeric Max number of QCs used to |
... |
parameters to be passed to database functions |
list of length 2 EIC indices for the ion duplicate plots
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | library(LUMA)
if(require(lcmsfishdata, quietly = TRUE)) {
file <- system.file("extdata","CAMERA_objects_Pos.Rdata", package =
"lcmsfishdata") # is case sensitive on Linux
load(file, envir = environment())
file2 <- system.file("extdata","CAMERA_objects_Neg.Rdata", package =
"lcmsfishdata") # is case sensitive on Linux
load(file2, envir = environment())
Peak.list <- lcmsfishdata::Peaklist_db[["Peaklist_Combined_with_Duplicate_IDs"]]
test <- plot_ionduplicate(anposGa = anposGa, annegGa = annegGa, Peak.list =
Peak.list, gen.plots = FALSE)
class(test) ##is list
length(test) ## with 2 elements
## Not run:
#Runs with pdf plotting. This requires access to raw datafiles and won't
#work with lcmsfishdata. Better to use your own data here.
test <- plot_ionduplicate(anposGa = anposGa, annegGa = annegGa, Peak.list =
Peak.list, gen.plots = TRUE)
## End(Not run)
}
|
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