visualizeFeatureSpline: Visualize the feature trajectory with the fitted Splines

Description Usage Arguments Value References Examples

Description

Plot the longitudinal features along with the fitted splines

Usage

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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 (ametwall@stanford.edu)

Examples

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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())

OmicsLonDA documentation built on Nov. 8, 2020, 5:50 p.m.