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())