NEWS

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SMARTTR 1.0.1

• To adhere to CRAN naming policy, we are changing our package repository name to SMARTTR. The new package website can be assessed here. Listed below is the previous changelog of SMARTR.

SMARTR 0.0.0.9000

• First release of SMARTR

SMARTR 1.0.0

• Major change in the way area/volume of regions is calculated to account for bug in underlying atlas in wholebrain that pulls the wrong region registration outlines for certain subregions. Specifically, areas such as the DG-sg and DG-mo are represented twice in the same atlas plate when the hippocampus curves rostral-caudally. Previously only one of the two subregion outlines were used to calculate area, which should now be fixed.
• Change in the exclude_anatomy, get_registered_volumes, and normalize_cell_counts functions to include a simplify_keywords parameter which automatically re categorizes subregions to their major parent regions based on specific keywords.
• Modified the normalize_cell_counts and combine_cell_counts function to also store counts and areas/volume by slice in the mouse and experiment objects, respectively. This allows for easy evaluation of the raw mapped dataset.
• Our various analysis and visualization function are now compatible with the Kim lab's unified atlas. The unified atlas synthesizes label from two of the most highly used atlases --Franklin-Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute.Check out the various help pages for analysis and plotting functions to see which ones now includeontology as a relevant parameter. Simply change the value from allen to unified to process datasets using this ontology.
• New function simplify_cell_count can process external datasets and simplify regions based on keywords. Simplification is based on user indicated atlas (allen or unified)

SMARTR 1.0.1

• New function export_permutation_results reformats permutation results and saves it nicely for users.
• Tables are now saved into an autocreated tables folder in the output directory for organization.
• Added create_joined_networks and plot_joined_networks as as capability to visualize the overlapping edges in two networks with outer joined nodes. The capability to export a list of overlapping edges between the joined network is included as a parameter in create_joined_networks. See the documentation for more details.
• Altered plot_correlation_heatmaps() function to automatically plot parent regions as subfacets

SMARTTR 1.0.2

• Added rewire_network() function to implement maslov sneppen rewiring to generate null networks. Added summarize_null_networks() function to summarize the output of multiple rewiring iterations.
• Added patch for bug in the create_joined_networks() function
• Added filter isolates option for networks. This allows isolated nodes to be retained for global calculations and retains the same node numbers between networks.
• Added import_mapped_datasets() as a way to import an externally mapped dataset and check_ontology_coding() to check the ontology coding of an imported dataset. A tutorial on how to use these function are documented on our article titled Importing External Datasets.
• Added new progress bar display option for the permutation analysis function correlation_diff_permutation()
• Added new feature to plot a permutation difference network using plot_perm_diff_network().
• Added new heatmap plotting options allow for viridis color scheme and new custom faceting colors for parent regions using ggh4x
• Bug fixes in plot_normalized_counts(), volcano_plot(), normalize_cell_counts()