Package index
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cell.level_boxplots() - Data visualization: individual morphology measures
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celldensity() - Calculate microglia density
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clusterfeatures() - Cluster-specific average morphology measures
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clusterpercentage() - What are your morphology cluster percentages across variables of interest?
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clusterpercentage_boxplots() - How do morphology cluster percentages vary across variables of interest?
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clusterplots() - Plot to show morphology clusters in PC space
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data_1xLPS_mouse - 1xLPS mouse dataset
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data_2xLPS_mouse - 2xLPS mouse dataset
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data_2xLPS_mouse_fuzzykmeans - 2xLPS fuzzy k-means soft clustering dataset
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data_ImageTypeComparison - ImageTypeComparisons mouse dataset
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featurecorrelations() - Correlation heatmap across morphology features
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featurecorrelations_stats() - Underlying stats for correlation heatmap across morphology features
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fraclac_tidying() - Tidy up your FracLac output
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logscale() - Log scale
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merge_data() - Merge FracLac and AnalyzeSkeleton results together into one final cell-level data frame
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metadata_columns() - Tidy up metadata
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minmax() - Min-max scaling
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normalize_logplots() - Exploratory data analysis: normalization methods
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normalize_minmax() - Exploratory data analysis: min-max scaled plots
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normalize_scaled() - Exploratory data analysis: scaled plots
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outliers_boxplots() - Exploratory data analysis: outlier detection
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outliers_distributions() - Exploratory data analysis: outlier detection
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pcadata() - Dimensionality reduction using PCA
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pcadata_elbow() - Dimensionality reduction using PCA and elbow/scree plot to get variance explained
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pcfeaturecorrelations() - What morphology features describe the PCs?
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pcfeaturecorrelations_stats() - Underlying stats for correlation heatmap exploring which morphologies describe the PCs
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plots_expvariable() - Explore how experimental variables describe data
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samplesize() - Sample size
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skeleton_tidying() - Concatenate your individual AnalyzeSkeleton output files into one dataframe
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stats_cluster.animal() - Stats analysis: cluster-level changes
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stats_morphologymeasures.animal() - Stats analysis: individual morphology measures
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transform_log() - Transform data: Log scale
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transform_minmax() - Transform data: Min-max scaling
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transform_scale() - Transform data: Scaling