In yongkee/oneSENSE: One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)

Installing and Loading the Package

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To install oneSENSE package, start R and run the following code:

source("https://bioconductor.org/biocLite.R") biocLite("oneSENSE")

Load the package with the following code

library(oneSENSE)

Read the package description to find out more about oneSENSE GUI

? "onesense_GUI()"

Using the oneSENSE package

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Rational of One-SENSE

One-SENSE measures cellular parameters assinged to manually predefined catergories, and a one-dimensional map is constructed for each catergory using t-SNE. Each dimension is informative and can be annotated through the use of heatplots aligned in parallel to each axis, allowing for simultaneous visualization of two catergories across a two-dimensional plot. The cellular occupancy of the resulting plots alllows for direct assessment of the relationships between the categories.

Read more about One-SENSE: here

Run oneSENSE using the GUI

The easiest way to access oneSENSE is via the Graphics User Interface(GUI) provided in the package. After loading the package, simply set the directory as instructed in the note above and run the following code:

onesense_GUI()

The interface will appear like below, you can click the information button ! to check the explanation for each entry and customize your own analysis.

1. Choose the directory where the FCS files are located.
2. Select the FCS files you want to use for analysis.
3. Select the first, second and/or third(optional) category of markers you want to group together
4. Input the number of cells you want to subsample from each FCS file.
5. Input the number of bins you want for the cells to be sorted into
6. Press submit and it will run to produce median heatplots
7. If you wish to do a frequency heatmap, press select coordinates and then run press frequency heatplots.

Depending on the size of your data, it will take some time to run the analysis. Once done, the oneSENSE visualisations will be displayed.

yongkee/oneSENSE documentation built on May 5, 2019, 9:03 p.m.