Understanding how the cells' anatomical location and spatial molecular distribution determine the cellular response to a high-caloric diet requires developing machine-learning methods for analysis and visualization.
The R-package Csppa employs machine learning for cellular spatial point pattern analysis and visualization. Hence, Csppa allows a comprehensive understanding of spatial and temporal changes of particular cellular gene expression during different time points of adaptation to a high-caloric diet.
Here we focus on the astrocytes from the arcuate nucleus of the mouse brain and the expression of Gfap and Aldh1l1 genes recovering spatial point patterns under standard chow (SC), 5 and 15-day high fat high sugar (HFHS) diet. The R-package Csppa allows for assessing whether these astrocyte populations are spatially organized and whether they tend to form local identical clusters in response to an HFHS diet over time. To do that, the algorithm measures the degree of spatial coherence (depicting the level of similarity between neighbors) of each astrocytic sub-type in different conditions (SC, 5d, or 15d HFHS diet) by applying Moran I spatial autocorrelation coefficient, previously described as an indicator of the level of spatial dispersion. On top of that, employing a random forest classifier determines the partitioning of the feature space shared by astrocytes expressing Gfap and Aldh1l1 in each experimental group.
The package Csppa depends on spatstat and on R >= 3.0.0 and is available from GitHub. This requires the package devtools:
devtools::install_github("viktormiok/Csppa", build_vignettes=TRUE)Please restart R before loading the package and its documentation:
library(Csppa)
utils::help(Csppa)
utils::vignette("Csppa")Data required for cellular spatial point pattern analysis will be deposited online soon:
| Data type | Data link |
|---|---|
| Aldh1l1 only | link |
| Gfap only | link |
| Double positive | link |
Please see the following tutorials for detailed examples of how to use Csppa:
Csppa is distributed under the MIT license. Please read the license before using Csppa, distributed in the LICENSE file.
Publications related to Csppa include:
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Lutomska, L.M., Miok, V., Krahmer, N., González García, I., Gruber, T., Le Thuc, O., De Bernardis Murat, C., Legutko, B., Sterr, M., Saher, G., Lickert, H., Ussar, S., Tschöp, M., Lutter, D., García-Cáceres, C. (2022), Diet triggers specific responses of hypothalamic astrocytes in time and region dependent manner, Glia 70 (10), 1795-2008.
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Lutomska, L.M., Miok, V., Krahmer, N., González García, I., Gruber, T., Le Thuc, O., De Bernardis Murat, C., Legutko, B., Sterr, M., Saher, G., Lickert, H., Ussar, S., Tschöp, M., Lutter, D., García-Cáceres, C.(2021), Hypercaloric diet selectively triggers a transient molecular rearrangement of astrocytes in the arcuate nucleus, bioRxiv, 4(1).
Please cite the relevant publications if you use Csppa.