visualizeFeatureSpline: Visualize the feature trajectory with the fitted Splines

In aametwally/OmicsLonDA: Omics Longitudinal Differential Analysis

Description

Plot the longitudinal features along with the fitted splines

Usage

visualizeFeatureSpline(se_object = NULL, omicslonda_object = NULL,
  fit.method = "ssgaussian", text = "FeatureName", unit = "days",
  ylabel = "Normalized Count", col = c("blue", "firebrick"),
  prefix = "Test")

Arguments

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

Value

null

References

Ahmed Metwally ([e-mail])

Examples

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())

aametwally/OmicsLonDA documentation built on Feb. 10, 2020, 11:47 a.m.