title: 5-HT Transcriptomic
emoji: 🧠
colorFrom: gray
colorTo: green
sdk: docker
pinned: false
license: cc-by-4.0
The data within the "Data" folder is subject to CC BY-NC 4.0, as specified by the original authors https://alleninstitute.github.io/abc_atlas_access/descriptions/WMB_dataset.html.
The 'Spatial MERFISH' and 'Overview genes by brain structure' are associated with the MERFISH dataset, remaing tabs are associated with the RNA-seq dataset. Each tab is associated to different interactive controls and panels. More details in the associated manuscript.
'Spatial MERFISH':
5 interactive controls enable the selections of different datasets from {Zhang, 2023 #2887}, brain section, gene, class and subclass. The datasets available are 2 coronal (Zhuang-ABCA-1/2) and 2 sagittals (Zhuang-ABCA-3/4). The brain section selector enables the visualization of different slices. The gene selector enables the selection of a specific gene. Class and subclass selector restrict the visualization to selected groups. 6 panels are provided. From top to bottom: lineplot representing the proportion of cells selected out the cells available across the spatial axis associated to each dataset, lineplot representing the amount of transcription across space of the selected gene, lineplot representing the percentage of cells across space in which RNA of the selected gene was detected (threshold set at 0.3), barplot representing the percentage of Htr positive cells in the selected slice grouped by brain structure (number in each bar is the absolute number of cells) and two panels representing the slice selected with the gene transcription on the left and atlas metadata on the right.
'Gene by class/subclass/supertype/cluster':
2 interactive controls enable the selections of neighborhood group and gene. The neighborhood selector enables the selection of a specific neighborhood. The gene selector enables the selection of a specific gene. For each class of neurons we provide 3 levels of visualization. On top, violinplots representing the gene prevalence by subclass; in the middle, violinplots representing prevalence by supertype and on the bottom barplots representing prevalence by cluster. Each subclass is color-coded according to the panel available for each class.
'Overview genes by class':
4 interactive controls enable the selections of class, subclass, type of grouping and sorting. The class and subclass selectors enable the selection of a specific class and subclass, respectively. The plot can begrouped at different levels of detail: classes, subclasses, supertypes and even individual clusters (the number of groups that can visualized at the same time is limited by the maximum recursion depth of Holoviews). The plot can be sorted by the group´s alphabetical name or gene expression. Gene prevalence is represented with a heatmap in which the colorbar is updated according to the limits of the current selection. Y axis is populated by the name of the groups selected by the "Group by" selector. X axis shows each Htrs.
'Overview genes by brain structure':
2 interactive controls enable the selections of division and neurotransmitter. The division and neurotransmitter selectors enable the selection of a specific brain division and neurotransmitter, respectively. Gene prevalence is represented with a heatmap in which the colorbar is updated according to the limits of the current selection. Gene prevalence is limited to cluster enriched in the according gene (prevalence within cluster of the gene >70%). The y axis is populated by the brain structures belonging to the currently selected brain division. For each division we can refine our selection by isolating neurons releasing a specific neurotransmitter. X axis shows each Htrs.