'plotting' 검색 결과

Run empirical and causal analyses in Python with StatsPAI, from stating assumptions to estimating effects and checking how results change under alternative choices. Produce diagnostic figures, regression tables, and replication bundles for economics, public health, or machine learning studies.

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• Estimating policy or intervention effects
• Comparing public health effect estimates
• Examining how effects differ across groups

Build Python code for economic models and policy evaluation, with guidance on choosing libraries, estimating effects, plotting results, and checking robustness. Covers macroeconomic simulation and causal inference, the analysis of cause and effect.

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• Implementing macroeconomic models in Python
• Estimating policy effects with difference-in-differences
• Checking assumptions and robustness in causal analysis

Use this skill whenever the user asks for a chart, graph, plot, or visualization of data — 'chart this by month', 'show me a breakdown by category', 'visualize the trend'. Covers picking the right chart type for the question being asked, labeling/readability rules, and which plotting library to reach for. Pair with data-analysis for the underlying data prep.

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Processes and analyzes data with resident-kernel engines (DuckDB, Polars) and one-shot tools. Use for CSV/parquet/JSON analysis, group-by/join/aggregation, time series, distributions, cleaning, or plotting a dataset.

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Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.

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A low-level plotting library for comprehensive customization. Use when fine-grained control over every plot element is needed, creating new types of charts, or integrating into specific scientific workflows. Can export to PNG/PDF/SVG for publication. For quick statistical charts, use seaborn; for interactive charts, use plotly; for journal-style, publication-ready multi-panel charts, use scientific-visualization.

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Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.

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Use when evaluating the clinical utility of a binary prediction model from a single clinical CSV file by fitting a logistic decision-curve model, plotting decision and clinical-impact curves, and exporting summary outputs. NOT for: survival calibration, ROC-only discrimination analysis, nomogram construction, or time-to-event outcomes.

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Synthesize new waveforms from scratch for Simulink inports using createInputDataset. Use ONLY when the user asks to generate, create, or synthesize signals (step, ramp, sine, chirp, pulse, noise) to populate a Dataset for External Inputs or Signal Editor. Covers timeseries and timetable formats with correct data type, interpolation, units, and dimensions. Also covers function-call and trigger inport timing setup. Do NOT use when the user wants to load, import, or read existing data from files (MAT, CSV, spreadsheet) — even if that data will be used as model input. Do NOT use for running simulations or plotting outputs.

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Renders Hi-C contact matrices honestly and reproducibly with matplotlib, cooltools, HiCExplorer, pyGenomeTracks, FAN-C, CoolBox, and plotgardener. Covers the raw/ICE-balanced/observed-over-expected transform choice, LogNorm vs symmetric-diverging colormaps with vmax/percentile clipping, resolution-to-feature matching (compartments 100-500kb, TADs 10-40kb, loops 5-10kb), square vs rotated-triangle track-stacking, NaN/white-stripe handling, virtual 4C, APA/saddle/on-diagonal pileups, two-condition side-by-side and log2-ratio maps, and interactive (HiGlass) vs scripted-static publication figures. Use when plotting a contact matrix, choosing a normalization or color scale, building a multi-track Hi-C figure, making a virtual 4C profile, piling up loops/boundaries, or comparing two conditions.

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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (log2 IP/input bigWig via deepTools bamCompare; pyGenomeTracks; Gviz; IGV/UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), feature-distribution stacked bars, and volcano/MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012; Meyer 2012). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features, generating DRACH motif logos as sanity checks, rendering volcano plots of differential m6A, or reproducing the stop-codon enrichment plot.

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Build publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout, rcParams customization, TrueType (Type-42) font embedding for journal submission, and CVD-safe palettes. Covers seaborn integration, common chart types, axis formatting, and the small gotchas that distinguish reproducible matplotlib from notebook scratch. Use when producing publication figures in Python — RNA-seq scatter, single-cell embeddings, generic biological plotting.

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Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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Implement, review, or improve data visualizations using Swift Charts. Use when building bar, line, area, point, pie, donut, or iOS 26 3D charts; when adding chart selection, scrolling, annotations, axes, scales, legends, or foregroundStyle grouping; when plotting functions with BarPlot, LinePlot, AreaPlot, PointPlot, Chart3D, or SurfacePlot; or when creating heat maps, Gantt charts, grouped bars, sparklines, threshold lines, or spatial visualizations.

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Create and customize MATLAB charts and plots. Plot types (line, scatter, bar, histogram, heatmap, surface), axes configuration, annotations, data tips, interactive plots, animation, multiple axes with tiledlayout, colororder, and performance optimization. Works for standalone figures, Live Scripts, and uifigure apps. Use when plotting data, customizing axes, adding annotations or interactivity, animating charts, or arranging multiple axes. Triggers: plot, chart, graph, axes, uiaxes, annotation, data tips, animation, tiledlayout, colororder, heatmap, scatter, figure, visualization, export.

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Use this skill when fitting accelerated life models, computing mean time to failure (MTTF), B10 life and similar quantities, fitting life distributions like Weibull for reliability analysis, comparing distribution fits, computing confidence intervals on reliability quantities with bootstrapping, performing lifetime prediction, computing failure rates, plotting Kaplan-Meier curves, computing survival functions, or doing reliability analysis.

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Generate Euro NCAP test scenarios and variants using the ADT Euro NCAP support package. Use when creating NCAP seed scenarios, generating variants, translating between drivingScenario and RoadRunner, plotting scenario descriptors, computing NCAP scores, or exporting reports. Triggers on: ncapScenario, euroAssessment, getScenario, getScenarioDescriptor, generateVariants, ScenarioDescriptor, ScenarioDescriptorPlot, ncapScore, ncapReport, exportReport, configureVUT, assessmentTable, Euro NCAP, CCRs, CCRm, CCRb, CCFtap, CCCscp, CPNA, CPFA, CBNA, variant generation.

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sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.

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Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <d

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A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).

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'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

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Functions for plotting genomic data

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Step 1 of the PaperOrchestra pipeline (arXiv:2604.05018). Convert (idea.md, experimental_log.md, template.tex, conference_guidelines.md) into a strict JSON outline containing a plotting plan, literature search plan (Intro + Related Work), and section-level writing plan with citation hints. TRIGGER when the orchestrator delegates Step 1 or when the user asks to "outline a paper from raw materials" or "generate the paper structure".

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Orchestrate the full PaperOrchestra (Song et al., 2026, arXiv:2604.05018) five-agent pipeline to turn unstructured research materials (idea, experimental log, LaTeX template, conference guidelines, optional figures) into a submission-ready LaTeX manuscript and compiled PDF. TRIGGER when the user asks to "write a paper from my experiments", "turn this idea and these results into a paper", "generate a conference submission", "run paper-orchestra on X", or otherwise wants the end-to-end paper-writing pipeline. Coordinates the outline-agent, plotting-agent, literature-review-agent, section-writing-agent, and content-refinement-agent skills.

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