| visualizeFeatureSpline {OmicsLonDA} | R Documentation |
Plot the longitudinal features along with the fitted splines
visualizeFeatureSpline(se_object = NULL, omicslonda_object = NULL,
fit.method = "ssgaussian", text = "FeatureName", unit = "days",
ylabel = "Normalized Count", col = c("blue", "firebrick"),
prefix = "Test")
se_object |
SummarizedExperiment object contains omics count/level matrix and metadata |
omicslonda_object |
The returned object from omicslonda analysis |
fit.method |
The fitting method (ssgaussian) |
text |
feature name |
unit |
time unit used in Time vector (hours, days, weeks, months, etc.) |
ylabel |
text to be shown on the y-axis of all generated figures (default: "Normalized Count") |
col |
two color to be used for the two groups (eg., c("red", "blue")). |
prefix |
prefix to be used to create directory for the analysis results |
null
Ahmed Metwally (ametwall@stanford.edu)
library(SummarizedExperiment)
data(omicslonda_data_example)
omicslonda_se_object_adjusted = adjustBaseline(
se_object = omicslonda_data_example$omicslonda_se_object)
omicslonda_test_object = omicslonda_se_object_adjusted[1,]
points = seq(1, 500, length.out = 500)
res = omicslonda(se_object = omicslonda_test_object, n.perm = 10,
fit.method = "ssgaussian", points = points, text = "Feature_1",
parall = FALSE, pvalue.threshold = 0.05,
adjust.method = "BH", time.unit = "days",
ylabel = "Normalized Count",
col = c("blue", "firebrick"), prefix = "OmicsLonDA_example")
visualizeFeatureSpline(se_object = omicslonda_test_object, omicslonda_object =
omicslonda_data_example$omicslonda_results, fit.method = "ssgaussian",
text = "Feature_1", unit = "days",
ylabel = "Normalized Count",
col = c("blue", "firebrick"),
prefix = tempfile())