# tomoseqr
`tomoseqr` is an R package for analyzing Tomo-seq (a method to obtain
genome-wide expression data with spatial resolution) data. The algorithm
of image reconstruction is based on [Junker et al, 2014.](#reference)
## Usage
### Installation
```{r}
library(devtools)
install_github("bioinfo-tsukuba/tomoseqr")
```
### Data preparation
Please prepare Tomo-seq data that meets the following requirements.
1. It is a `data.frame` object for each axis.
1. Its **first cloumn** has gene ID. It's not enough that only row
names indicate gene ID.
1. The order of the second and subsequent columns should be the same as
the order of the sections.
1. It has a header.
#### Data example
```{r}
gene_ID section1 section2 section3 section4
1 gene1 0.000000 0.0000 2867.75420 9086.81135
2 gene2 440.599448 531.7915 36.91591 484.06813
3 gene3 75.446821 833.9432 736.82367 559.89157
4 gene4 506.865166 930.0414 880.26654 52.85974
5 gene5 2.159842 271.6788 210.06446 445.08979
```
## Example usage
```{r}
library(tomoseqr)
data("testx", "testy", "testz", "mask")
tomo_obj <- Estimate3dExpressions(
testx,
testy,
testz,
mask=mask,
query=c("gene1", "gene2")
)
ImageViewer(tomo_obj, "gene1")
```
```{r}
Animate2d(tomo_obj, "gene1", target="unite")
```
## Reference
Junker et al. Genome-wide RNA Tomography in the Zebrafish Embryo.
*Cell*, 2014.
<https://doi.org/10.1016/j.cell.2014.09.038>
## Contact
Ryosuke Matsuzawa / [shingenmochi](https://github.com/shingenmochi)
