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     Quick Analysis Plan


    I can recreate a β€œcapsule-dependent infection chance” style barplot from the phiK2044 paper by converting the reported capsule-associated host-range counts into proportions (e.g., total lysable 17/81; hvKp lysed 14/31; ST23 lysed 7/8; K1 lysed 12/13), then plotting % lysed as the infection probability proxy.


     Long Analysis Plan


    Goal
    Recreate a capsule β€œinfection chance” barplot by extracting the paper’s capsule-linked host-range counts and converting them to % lysed (a direct, defensible proxy for β€œinfection probability” under the paper’s assay conditions).
    1) Identify the exact barplot definition (critical)
    The phrase β€œinfection chance capsules barplot” is ambiguous without the figure caption/text. I will therefore (i) use only quantities explicitly present in the provided paper-extract and (ii) label the plot as β€œ% lysed by phiK2044”, which matches the paper’s capsule-associated host-range testing and is directly computable. If your target figure uses a different denominator (e.g., probability of infection at a specific MOI/timepoint, or EOP-based probabilities), you must paste the figure caption or the paper text containing the plot’s formula.
    2) Extract the numeric β€œcapsule-associated” data from the paper
    From phiK2044 host-range testing, compute the following proportions:
    • Total: 17 lysed / 81 tested
    • hvKp: 14 lysed / 31 hvKp isolates
    • ST23: 7 lysed / 8 ST23 isolates
    • K1: 12 lysed / 13 K1 isolates
    These counts are reported directly in the extracted results summary.
    3) Compute proportions (% lysed)
    Percentages:
    • Total: 17/81 β‰ˆ 20.98765432098765%
    • hvKp: 14/31 = 45.2% (reported)
    • ST23: 7/8 = 87.5% (reported)
    • K1: 12/13 β‰ˆ 92.3% (reported)
    (Where the paper already provides percentages, we keep them consistent with the reported values.)
    Recreated barplot (Plotly)
    What this plot is (and is not)
    • Is: a direct conversion of the paper’s capsule/subtype-associated host-range lysing counts into % lysed.
    • Is not: a time-resolved infection probability model (unless that’s exactly what the paper figure does). The plot does not incorporate MOI/time dependence, EOP, or pharmacokinetic factorsβ€”because those are not provided for this specific β€œinfection chance” axis in the extracted text.
    The paper also supports the biological link that phiK2044 tropism is capsule-mediated via wcaJ-regulated capsule binding (and that wcaJ knockout confers resistance), which justifies using capsule-linked host-range subsets as the x-axis categories.
    4) Coding/data workflow plan (rigorous + reproducible)
    1. Parse the paper-extract source: store the exact numerator/denominator counts (lys ed and tested totals per category) in a structured table (CSV/JSON) tagged with the citation DOI.
    2. Standardize the β€œinfection proxy”: define y = 100 * lysed/tested. Keep reporting as β€œ% lysed” to avoid overstating as true infection probability.
    3. Propagate uncertainty (recommended): compute binomial 95% CIs for each proportion using a conservative method (e.g., Wilson score) so the bar heights are interpretable statistically. (This step requires counts only; it’s not in the extracted text, but it’s compatible with it.)
    4. Recreate plot styling: match the paper’s category order and bar colors if the figure is available; otherwise use a clean publication style (accent color #0C3576, clear axis labels, outside count labels).
    5. Validation check: ensure computed percentages exactly match the paper’s reported values for hvKp (45.2%), ST23 (87.5%), and K1 (92.3%) within rounding.
    5) Potential blind spots / limitations (skeptical audit)
    • Figure mismatch risk: the target barplot might use a different definition of β€œinfection chance” than % lysed. Without the figure caption or the exact formula, we can only recreate a defensible proxy from host-range lysing counts.
    • Selection bias in isolate sets: the paper tests 81 clinical isolates; if isolate composition differs from the original figure’s cohort, the bar heights will differ.
    • Overinterpretation risk: % lysed is an in vitro host-range outcome, not necessarily a probability of successful infection across conditions (MOI, time, environment).
    • Confidence in mechanistic link: the wcaJ knockout/complementation supports capsule dependence, but the plot still collapses multiple biological steps (adsorption, replication, lysis) into a single binary readout per isolate.
    Make this match the paper exactly
    Paste the exact figure caption or the β€œinfection chance” equation used in the paper. Then I’ll: (i) swap categories if needed, (ii) use the correct denominator/timepoint, and (iii) reproduce styling (order, labels, CI bars if present).


    Feedback:    

    Updated: April 27, 2026

     Top Data Sources ExportMCP


     Analysis Wizard



    Computes % lysed = 100Β·(lys ed/total) from phiK2044 capsule-linked host-range counts, then generates a publication-style barplot with exact value labels for Total, hvKp, ST23, and K1.



     Hypothesis Graveyard


    Assuming β€œinfection chance” literally equals % lysed in all capsule figures is unsafe; without the caption/formula, that assumption can be falsified by mismatched denominators (e.g., typeable vs total, specific timepoint, or EOP thresholding).

     Science Art


    Analyze Data: recreate infection chance capsules barplot from paper text Science Art

     Science Movie


    Make a narrated HD Science movie for this answer ($32 per minute)




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