Add BVBRC statistics R Markdown document by AbhirupaGhosh · Pull Request #13 · JRaviLab/amRdata

AbhirupaGhosh · 2026-03-05T22:29:23Z

Description

What kind of change(s) are included?

Feature (adds or updates new capabilities)
Bug fix (fixes an issue).
Enhancement (adds functionality).
Breaking change (these changes would cause existing functionality to not work as expected).

Checklist

Please ensure that all boxes are checked before indicating that this pull request is ready for review.

I have read and followed the CONTRIBUTING.md guidelines.
I have searched for existing content to ensure this is not a duplicate.
I have performed a self-review of these additions (including spelling, grammar, and related).
I have added comments to my code to help provide understanding.
I have added a test which covers the code changes found within this PR.
I have deleted all non-relevant text in this pull request template.
Reviewer assignment: Tag a relevant team member to review and approve the changes.

jananiravi

needs the following to serve as a vignette

to reside in vignettes/
call specific tidyverse packages (bioc requirement)
check path for bvbrc_data.tsv & bvbrc vs. bvbrc_clean
use of named r chunks
text description between chunks
missing YAML
documentation
cc: @AbhirupaGhosh @eboyer221

jananiravi

needs annotation (text around code chunks)

eboyer221

Suggested code changes to format the vignette shown in review.
Additional comment : The Rmd should live at vignettes/BVBRC_stats.Rmd rather than doc/ (R packages auto-generated doc/ from vignettes/ at build time).

eboyer221 · 2026-05-14T19:16:20Z

+```{r setup, include=FALSE}
+library(tidyverse)
+
+bvbrc <- read.table("bvbrc_data.tsv", sep = "\t", header = TRUE, fill = TRUE, 


where is this file , 'bvbrc_data.tsv', coming from? does the user export it from BV-BRC? Right now I don't think the Rmd will work for anyone without that file.

eboyer221 · 2026-05-14T19:40:20Z

+---
+title: "bvbrc_stats"
+author: "Abhirupa"
+date: "`r Sys.Date()`"
+output: html_document
+---


Suggested change

---

title: "bvbrc_stats"

author: "Abhirupa"

date: "`r Sys.Date()`"

output: html_document

---

---

title: "BV-BRC Metadata Statistics"

author: "Abhirupa Ghosh"

date: "`r Sys.Date()`"

output: rmarkdown::html_vignette

vignette: >

%\VignetteIndexEntry{BV-BRC Metadata Statistics}

%\VignetteEngine{knitr::rmarkdown}

%\VignetteEncoding{UTF-8}

---

Bioconductor vignette-style header with the vignette: block so R recognizes it as a package vignette.

eboyer221 · 2026-05-14T19:42:14Z

+---
+
+```{r setup, include=FALSE}
+library(tidyverse)


Suggested change

library(tidyverse)

library(dplyr)

library(stringr)

library(purrr)

library(tibble)

Bioconductor does not want library(tidyverse) import if we can just import the parts that are actually used.

eboyer221 · 2026-05-14T19:44:30Z

+col_stats <- tibble(column = colnames(bvbrc)) %>%
+  mutate(
+    n_total   = nrow(bvbrc),
+    n_missing = map_int(column, ~ sum(is.na(bvbrc[[.x]]))),
+    n_present = n_total - n_missing,
+    pct_missing = 100 * n_missing / n_total,
+    n_distinct_non_missing = map_int(column, ~ n_distinct(bvbrc[[.x]], na.rm = TRUE))
+  ) %>%
+  arrange(desc(pct_missing), column)


Suggested change

col_stats <- tibble(column = colnames(bvbrc)) %>%

mutate(

n_total = nrow(bvbrc),

n_missing = map_int(column, ~ sum(is.na(bvbrc[[.x]]))),

n_present = n_total - n_missing,

pct_missing = 100 * n_missing / n_total,

n_distinct_non_missing = map_int(column, ~ n_distinct(bvbrc[[.x]], na.rm = TRUE))

) %>%

arrange(desc(pct_missing), column)

col_stats <- tibble(column = colnames(bvbrc_clean)) %>%

mutate(

n_total = nrow(bvbrc_clean),

n_missing = map_int(column, ~ sum(is.na(bvbrc_clean[[.x]]))),

n_present = n_total - n_missing,

pct_missing = 100 * n_missing / n_total,

n_distinct_non_missing = map_int(column, ~ n_distinct(bvbrc_clean[[.x]], na.rm = TRUE))

) %>%

arrange(desc(pct_missing), column)

currently, col_stats is using bvbrc, but the stats below use bvbrc_clean so that the missing values are accounted for. Suggesting changing from bvbrc -> bvbrc_clean here so that it is consistent if that is appropriate.

eboyer221 · 2026-05-14T19:45:38Z

+  arrange(desc(pct_missing), column)
+```
+
+```{r}


Suggested change

```{r}

``````{r col_stats_output}

eboyer221 · 2026-05-14T19:45:54Z

+# --- Outputs -----------------------------------------------------------------
+cat("\n--- Per-column stats (whole table) ---\n"); print(col_stats, n = Inf)
+```
+```{r}


Suggested change

```{r}

``````{r host_block_output}

eboyer221 · 2026-05-14T19:46:10Z

+```{r}
+cat("\n--- Host block stats ---\n");           print(host_block_stats)
+```
+```{r}


Suggested change

```{r}

``````{r geo_block_output}

eboyer221 · 2026-05-14T19:46:25Z

+```{r}
+cat("\n--- Geographic block stats ---\n");     print(geo_block_stats)
+```
+```{r}


Suggested change

```{r}

``````{r diag_output}

eboyer221 · 2026-05-14T19:52:00Z

+)
+```
+
+```{r functions}


Each of these code chunks needs a paragraph saying what it computes and why. Need to add a paragraph before this functions chunk, before stats (line 84), and before each of the four output chunks (lines 134-145).

These changes should resolve #13 (review)

AbhirupaGhosh and others added 2 commits March 5, 2026 15:29

Add BVBRC statistics R Markdown document

518d6e5

Style code (GHA)

7dca3bf

jananiravi reviewed Apr 13, 2026

View reviewed changes

jananiravi requested a review from eboyer221 April 13, 2026 20:43

jananiravi reviewed Apr 15, 2026

View reviewed changes

eboyer221 requested changes May 14, 2026

View reviewed changes

----
-title: "bvbrc_stats"
-author: "Abhirupa"
-date: "`r Sys.Date()`"
-output: html_document
----
+---
+title: "BV-BRC Metadata Statistics"
+author: "Abhirupa Ghosh"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{BV-BRC Metadata Statistics}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---

-library(tidyverse)
+library(dplyr)
+library(stringr)
+library(purrr)
+library(tibble)

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AbhirupaGhosh commented Mar 5, 2026

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eboyer221 May 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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eboyer221 May 14, 2026 •

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