Tutorial_Revelio.Rmd

---
title: "Tutorial"
output:
  html_document:
    code_folding: hide
    df_print: paged
    toc: no
    toc_depth: 4
    toc_float: true
---

```{r}
library(Revelio)
myData <- createRevelioObject(rawData = revelioTestData_rawDataMatrix,
                              cyclicGenes = revelioTestData_cyclicGenes)
```

```{r}
myData <- getCellCyclePhaseAssignInformation(dataList = myData)
```

```{r}
myData <- getPCAData(dataList = myData,
                     boolPlotResults = TRUE)
```

```{r}
myData <- getOptimalRotation(dataList = myData,
                             boolPlotResults = TRUE)
```

```{r}
normalizedDataWithoutCCEffects <- removeCCEffects(dataList = myData)
```

```{r}
myData <- getVelocityMatrix(dataList = myData,
                            rawIntronicData = revelioTestData_rawIntronicMatrix)
```

```{r}
myData <- getPCAData(dataList = myData,
                     boolPlotResults = FALSE)
myData <- getOptimalRotation(dataList = myData,
                             boolPlotResults = TRUE)
```

```{r}
myData <- getExtrapolatedStateInDCSpace(dataList = myData)
```

```{r}
myData <- getVelocityGridCC(dataList = myData,
                            sigma = 0.6,
                            numberOfGridPointsOneSide = 20,
                            boolPlotResults = TRUE)
```

```{r}
myData <- plotVelocityOnAveragedTrajectory(dataList = myData,
                                           numberOfAnchors = 10)
```

```{r}
myData <- getVelocityGridAlongThirdDimensions(dataList = myData,
                                              whichThirdDimension = 3,
                                              sigma = 1.5,
                                              numberOfGridPointsOneSide = 20,
                                              boolPlotResults = TRUE)
```