visualizeFeatureSpline {OmicsLonDA} | R Documentation

## Visualize the feature trajectory with the fitted Splines

### 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 (ametwall@stanford.edu)

### 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())

[Package OmicsLonDA version 1.8.0 Index]