object_config {LorMe} | R Documentation |
Set taxonomy summary configuration
Description
This function set taxonomy summary configuration by assigning treatment column number, facet column number, replication column number, treatment mapping color, treatment order and facet order.
Usage
object_config(
taxobj,
treat_location,
facet_location = NULL,
rep_location,
subject_location = NULL,
treat_col = NULL,
treat_order = NULL,
facet_order = NULL
)
Arguments
taxobj |
Taxonomic summary object generated by |
treat_location |
Numeric. Treatment column number in metafile/groupinformation. |
facet_location |
Numeric, default:NULL. Facet column number in metafile/groupinformation. |
rep_location |
Numeric. Replication column number in metafile/groupinformation. |
subject_location |
Numeric, default:NULL.Subject column number in metafile/groupinformation (used for pairwise experiment). |
treat_col |
Named character string, default:NULL. A set of aesthetic character to map treatment to. |
treat_order |
Character string, default:NULL. The character string indicating treatment displaying order. |
facet_order |
Character string, default:NULL. The character string indicating facet displaying order. |
Value
object_config returns taxonomy summary object with configuration.
Author(s)
Wang Ningqi2434066068@qq.com
Examples
{
### Data preparation ###
data(testotu)
groupinformation <- data.frame(
group = c(rep("a", 10), rep("b", 10)),
factor1 = rnorm(10),
factor2 = rnorm(mean = 100, 10),
subject = factor(c(1:10, 1:10)),
group2 = c(rep("e", 5), rep("f", 5), rep("e", 5), rep("f", 5))
)
### Packaging metafile, community data, and taxonomy table ###
test_object <- tax_summary(
groupfile = groupinformation,
inputtable = testotu[, 2:21],
reads = TRUE,
taxonomytable = testotu[, c(1, 22)]
)
### Object configuration ###
test_object_plan1 <- object_config(
taxobj = test_object,
treat_location = 1,
rep_location = 4
)
### Facet configuration ###
test_object_plan2 <- object_config(
taxobj = test_object,
treat_location = 1,
rep_location = 4,
facet_location = 5
)
}