# Create a sample data frame for a pathology cohort
set.seed(42)
n_cases <- 150
crc_cases <- data.frame(
Histology = factor(sample(
c("Adenocarcinoma, NOS", "Mucinous Adenocarcinoma", "Signet Ring Cell Carcinoma"),
n_cases, replace = TRUE, prob = c(0.8, 0.15, 0.05)
)),
Differentiation = factor(sample(
c("Well", "Moderate", "Poor"),
n_cases, replace = TRUE, prob = c(0.2, 0.6, 0.2)
), ordered = TRUE, levels = c("Well", "Moderate", "Poor")),
MMR_Status = factor(sample(
c("pMMR", "dMMR", NA), # Include some missing data
n_cases, replace = TRUE, prob = c(0.80, 0.15, 0.05)
))
)
head(crc_cases)
#> Histology Differentiation MMR_Status
#> 1 Mucinous Adenocarcinoma Poor pMMR
#> 2 Mucinous Adenocarcinoma Moderate pMMR
#> 3 Adenocarcinoma, NOS Poor pMMR
#> 4 Mucinous Adenocarcinoma Moderate pMMR
#> 5 Adenocarcinoma, NOS Poor dMMR
#> 6 Adenocarcinoma, NOS Poor dMMRVignette: Generating Quick Summaries of Categorical Pathology Data
2025-06-03
Source:vignettes/reportcat.qmd
# This code simulates how the jamovi module would be called in an R environment.
# You would need the ClinicoPathDescriptives package installed.
# Load the library
library(ClinicoPathDescriptives)
#> Registered S3 method overwritten by 'future':
#> method from
#> all.equal.connection parallelly
#> Warning: replacing previous import 'dplyr::select' by 'jmvcore::select' when
#> loading 'ClinicoPathDescriptives'
# Run the reportcat analysis
results <- reportcat(
data = crc_cases,
vars = c("Histology", "Differentiation", "MMR_Status")
)
#>
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#> <tr><td headers="type" class="gt_row gt_left"><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:20px;width:20px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#4e79a7;overflow:visible;position:relative;"><path d="M40 48C26.7 48 16 58.7 16 72v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V72c0-13.3-10.7-24-24-24H40zM192 64c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zM16 232v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V232c0-13.3-10.7-24-24-24H40c-13.3 0-24 10.7-24 24zM40 368c-13.3 0-24 10.7-24 24v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V392c0-13.3-10.7-24-24-24H40z"/></svg></td>
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#> Adenocarcinoma, NOS, Mucinous Adenocarcinoma and Signet Ring Cell Carcinoma
#> </details></div></td>
#> <td headers="value" class="gt_row gt_center"><?xml version='1.0' encoding='UTF-8' ?><svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' width='141.73pt' height='34.02pt' viewBox='0 0 141.73 34.02'><g class='svglite'><defs> <style type='text/css'><![CDATA[ .svglite line, .svglite polyline, .svglite polygon, .svglite path, .svglite rect, .svglite circle { fill: none; stroke: #000000; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; } .svglite text { white-space: pre; } .svglite g.glyphgroup path { fill: inherit; stroke: none; } ]]></style></defs><rect width='100%' height='100%' style='stroke: none; fill: none;'/><defs> <clipPath id='cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg=='> <rect x='0.00' y='0.00' width='141.73' height='34.02' /> </clipPath></defs><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'></g><defs> <clipPath id='cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ=='> <rect x='1.00' y='2.99' width='139.74' height='20.62' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ==)'><rect x='133.28' y='3.93' width='7.45' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #DDEAF7;' /><rect x='108.13' y='3.93' width='25.15' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #91B4DA;' /><rect x='1.00' y='3.93' width='107.13' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #3181BD;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><text x='1.00' y='30.18' style='font-size: 8.00px; font-family: "Arial";' textLength='43.61px' lengthAdjust='spacingAndGlyphs'>3 categories</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right">0.0%</td></tr>
#> <tr><td headers="type" class="gt_row gt_left gt_striped"><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:20px;width:20px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#4e79a7;overflow:visible;position:relative;"><path d="M40 48C26.7 48 16 58.7 16 72v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V72c0-13.3-10.7-24-24-24H40zM192 64c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zM16 232v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V232c0-13.3-10.7-24-24-24H40c-13.3 0-24 10.7-24 24zM40 368c-13.3 0-24 10.7-24 24v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V392c0-13.3-10.7-24-24-24H40z"/></svg></td>
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#> <summary style='font-weight: bold !important;'>Differentiation</summary>
#> Moderate, Well and Poor
#> </details></div></td>
#> <td headers="value" class="gt_row gt_center gt_striped"><?xml version='1.0' encoding='UTF-8' ?><svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' width='141.73pt' height='34.02pt' viewBox='0 0 141.73 34.02'><g class='svglite'><defs> <style type='text/css'><![CDATA[ .svglite line, .svglite polyline, .svglite polygon, .svglite path, .svglite rect, .svglite circle { fill: none; stroke: #000000; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; } .svglite text { white-space: pre; } .svglite g.glyphgroup path { fill: inherit; stroke: none; } ]]></style></defs><rect width='100%' height='100%' style='stroke: none; fill: none;'/><defs> <clipPath id='cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg=='> <rect x='0.00' y='0.00' width='141.73' height='34.02' /> </clipPath></defs><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'></g><defs> <clipPath id='cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ=='> <rect x='1.00' y='2.99' width='139.74' height='20.62' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ==)'><rect x='119.31' y='3.93' width='21.43' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #DDEAF7;' /><rect x='97.88' y='3.93' width='21.43' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #91B4DA;' /><rect x='1.00' y='3.93' width='96.89' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #3181BD;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><text x='1.00' y='30.18' style='font-size: 8.00px; font-family: "Arial";' textLength='75.66px' lengthAdjust='spacingAndGlyphs'>3 categories, ordered</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right gt_striped">0.0%</td></tr>
#> <tr><td headers="type" class="gt_row gt_left"><svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:20px;width:20px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#4e79a7;overflow:visible;position:relative;"><path d="M40 48C26.7 48 16 58.7 16 72v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V72c0-13.3-10.7-24-24-24H40zM192 64c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zm0 160c-17.7 0-32 14.3-32 32s14.3 32 32 32H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H192zM16 232v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V232c0-13.3-10.7-24-24-24H40c-13.3 0-24 10.7-24 24zM40 368c-13.3 0-24 10.7-24 24v48c0 13.3 10.7 24 24 24H88c13.3 0 24-10.7 24-24V392c0-13.3-10.7-24-24-24H40z"/></svg></td>
#> <td headers="name" class="gt_row gt_left" style="font-weight: bold;"><div style='max-width: 150px;'>
#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>MMR_Status</summary>
#> pMMR and dMMR
#> </details></div></td>
#> <td headers="value" class="gt_row gt_center"><?xml version='1.0' encoding='UTF-8' ?><svg xmlns='http://www.w3.org/2000/svg' xmlns:xlink='http://www.w3.org/1999/xlink' width='141.73pt' height='34.02pt' viewBox='0 0 141.73 34.02'><g class='svglite'><defs> <style type='text/css'><![CDATA[ .svglite line, .svglite polyline, .svglite polygon, .svglite path, .svglite rect, .svglite circle { fill: none; stroke: #000000; stroke-linecap: round; stroke-linejoin: round; stroke-miterlimit: 10.00; } .svglite text { white-space: pre; } .svglite g.glyphgroup path { fill: inherit; stroke: none; } ]]></style></defs><rect width='100%' height='100%' style='stroke: none; fill: none;'/><defs> <clipPath id='cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg=='> <rect x='0.00' y='0.00' width='141.73' height='34.02' /> </clipPath></defs><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'></g><defs> <clipPath id='cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ=='> <rect x='1.00' y='2.99' width='139.74' height='20.62' /> </clipPath></defs><g clip-path='url(#cpMS4wMHwxNDAuNzR8Mi45OXwyMy42MQ==)'><rect x='119.78' y='3.93' width='20.96' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #DDEAF7;' /><rect x='1.00' y='3.93' width='118.78' height='18.75' style='stroke-width: 1.07; stroke: none; stroke-linecap: butt; stroke-linejoin: miter; fill: #3181BD;' /></g><g clip-path='url(#cpMC4wMHwxNDEuNzN8MC4wMHwzNC4wMg==)'><text x='1.00' y='30.18' style='font-size: 8.00px; font-family: "Arial";' textLength='43.61px' lengthAdjust='spacingAndGlyphs'>2 categories</text></g></g></svg></td>
#> <td headers="n_missing" class="gt_row gt_right">6.7%</td></tr>
#> </tbody>
#>
#>
#> </table>
#> </div>
#>
|
| | 0%
|
|......................................................................| 100%
# The results are HTML outputs that render directly in jamovi.
# In R, you would access them like this:
results$text # (for the text summary)
#>
#> Histology has 150 observations and 3 levels.
#> Adenocarcinoma, NOS: n = 115, 77% of valid cases.
#> Mucinous Adenocarcinoma: n = 27, 18% of valid cases.
#> Signet Ring Cell Carcinoma: n = 8, 5% of valid cases.
#> Missing values: 0.
#>
#> Differentiation has 150 observations and 3 levels.
#> Moderate: n = 104, 69% of valid cases.
#> Well: n = 23, 15% of valid cases.
#> Poor: n = 23, 15% of valid cases.
#> Missing values: 0.
#>
#> MMR_Status has 150 observations and 2 levels.
#> pMMR: n = 119, 85% of valid cases.
#> dMMR: n = 21, 15% of valid cases.
#> Missing values: 10.
results$text1 # (for the visual summary table)
#>
#> <table class="gt_table" data-quarto-disable-processing="false"
#> data-quarto-bootstrap="false">
#>
#> <tr class="gt_heading">
#> <td colspan="4" class="gt_heading gt_title gt_font_normal" style>.
#>
#> <tr class="gt_heading">
#> <td colspan="4" class="gt_heading gt_subtitle gt_font_normal
#> gt_bottom_border" style>150 rows x 3 cols
#>
#> <tr class="gt_col_headings">
#> <th class="gt_col_heading gt_columns_bottom_border gt_left"
#> rowspan="1" colspan="1" scope="col" id="type">
#> <th class="gt_col_heading gt_columns_bottom_border gt_left"
#> rowspan="1" colspan="1" scope="col" id="name">Column
#> <th class="gt_col_heading gt_columns_bottom_border gt_center"
#> rowspan="1" colspan="1" scope="col" id="value">Plot Overview
#> <th class="gt_col_heading gt_columns_bottom_border gt_right"
#> rowspan="1" colspan="1" scope="col" id="n_missing">Missing
#>
#>
#> <tbody class="gt_table_body">
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#> bold;"><div style='max-width: 150px;'>
#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>Histology
#> Adenocarcinoma, NOS, Mucinous Adenocarcinoma and Signet Ring Cell
#> Carcinoma
#>
#> <td headers="value" class="gt_row gt_center"><?xml version='1.0'
#> encoding='UTF-8' ?><svg xmlns='http://www.w3.org/2000/svg'
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#> <td headers="n_missing" class="gt_row gt_right">0.0%
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#> <details style='font-weight: normal !important;'>
#> <summary style='font-weight: bold !important;'>Differentiation
#> Moderate, Well and Poor
#>
#> <td headers="value" class="gt_row gt_center gt_striped"><?xml
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#> <td headers="type" class="gt_row gt_left"><svg aria-hidden="true"
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#> <summary style='font-weight: bold !important;'>MMR_Status
#> pMMR and dMMR
#>
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