Skip to content
This repository has been archived by the owner on Oct 2, 2024. It is now read-only.

Update PBTA ancestry cohort (3/N) #64

Merged
merged 3 commits into from
May 8, 2024
Merged

Update PBTA ancestry cohort (3/N) #64

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e243c74
update cohort and re-run modules
rjcorb Apr 16, 2024
b504eaa
Merge branch 'main' into rjcorb/62-update-cohort
rjcorb May 3, 2024
5e36ce6
fix alluvial plot
rjcorb May 3, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
31 changes: 27 additions & 4 deletions analyses/add-histologies/01-add_histologies.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,10 +52,13 @@ hist <- read_tsv(hist_file, guess_max = 1000000)
demographic data, pathology, and clinical data
```{r add histology}

# Add participant IDs to `ancestry`
# Add participant IDs and demographic data to `ancestry`
ancestry <- ancestry %>%
left_join(hist[,c('Kids_First_Biospecimen_ID', 'Kids_First_Participant_ID', 'sample_type', "cohort_participant_id")], by = 'Kids_First_Biospecimen_ID') %>%
dplyr::filter(sample_type != 'Tumor')
left_join(hist[,c('Kids_First_Biospecimen_ID', 'Kids_First_Participant_ID',
'sample_type', "cohort_participant_id",
'reported_gender', 'race', 'ethnicity')], by = 'Kids_First_Biospecimen_ID') %>%
dplyr::filter(sample_type != 'Tumor',
!grepl("-P|-M", cohort_participant_id))

# filter histologies file to exclude Normal samples
hist_tumor <- hist %>%
Expand All @@ -68,11 +71,19 @@ plot_mapping <- read_tsv(plot_mapping_file)
# add histology data to `ancestry` by participant ID
ancestry <- ancestry %>%
dplyr::left_join(hist_tumor[, c('Kids_First_Participant_ID', 'Kids_First_Biospecimen_ID_tumor', 'sample_id',
'reported_gender', 'race', 'ethnicity', 'broad_histology', 'cancer_group',
'broad_histology', 'cancer_group',
'molecular_subtype', 'tumor_descriptor', "CNS_region", 'extent_of_tumor_resection',
'age_at_diagnosis_days', 'OS_days', 'OS_status', 'EFS_days', "EFS_event_type",
'age_at_chemo_start', 'age_at_radiation_start')],
by = 'Kids_First_Participant_ID') %>%
# There is one sample (BS_M52K86E6) with no matched tumor in OPC v14, but is known to have an oligodendroglioma. We will manually enter braod_histology and cancer_group info
dplyr::mutate(broad_histology = case_when(
Kids_First_Biospecimen_ID == "BS_M52K86E6" ~ "Diffuse astrocytic and oligodendroglial tumor",
TRUE ~ broad_histology),
cancer_group = case_when(
Kids_First_Biospecimen_ID == "BS_M52K86E6" ~ "Oligodendroglioma",
TRUE ~ cancer_group)
) %>%
dplyr::left_join(plot_mapping[,c('broad_histology', 'cancer_group', 'plot_group')], by = c('broad_histology', 'cancer_group'))
```

Expand Down Expand Up @@ -100,6 +111,18 @@ ancestry_unique <- initial_tumors %>%
bind_rows(recurrent_tumors, other_tumors)
```

There is one sample (BS_6Z213H2V) with a matched tumor that is unassigned to a plot group but has high-confidence schwannoma by methylation subtyping. We will manually enter schwannoma classification, and assign any other remaining samples with no plot group to "Other tumor"

```{r}
ancestry_unique <- ancestry_unique %>%
dplyr::mutate(plot_group = case_when(
Kids_First_Biospecimen_ID_tumor == "BS_6Z213H2V" ~ "Schwannoma",
is.na(plot_group) ~ "Other tumor",
TRUE ~ plot_group
))

```


# Write merged data to file

Expand Down
80 changes: 44 additions & 36 deletions analyses/add-histologies/01-add_histologies.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -430,31 +430,18 @@ <h4 class="date">2023</h4>
<p>Load libraries and set directories</p>
<pre class="r"><code>library(data.table)
library(tidyverse)</code></pre>
<pre><code>## ── Attaching core tidyverse packages ──────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr 1.1.1 ✔ readr 2.1.4
## ✔ forcats 1.0.0 ✔ stringr 1.5.0
## ✔ ggplot2 3.4.2 ✔ tibble 3.2.1
## ✔ lubridate 1.9.2 ✔ tidyr 1.3.0
## ✔ purrr 1.0.1
## ── Conflicts ────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::between() masks data.table::between()
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::first() masks data.table::first()
## ✖ lubridate::hour() masks data.table::hour()
## ✖ lubridate::isoweek() masks data.table::isoweek()
## ✖ dplyr::lag() masks stats::lag()
## ✖ dplyr::last() masks data.table::last()
## ✖ lubridate::mday() masks data.table::mday()
## ✖ lubridate::minute() masks data.table::minute()
## ✖ lubridate::month() masks data.table::month()
## ✖ lubridate::quarter() masks data.table::quarter()
## ✖ lubridate::second() masks data.table::second()
## ✖ purrr::transpose() masks data.table::transpose()
## ✖ lubridate::wday() masks data.table::wday()
## ✖ lubridate::week() masks data.table::week()
## ✖ lubridate::yday() masks data.table::yday()
## ✖ lubridate::year() masks data.table::year()
## ℹ Use the conflicted package (&lt;http://conflicted.r-lib.org/&gt;) to force all conflicts to become errors</code></pre>
<pre><code>## ── Attaching packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.4.0 ✔ purrr 1.0.1
## ✔ tibble 3.1.8 ✔ dplyr 1.1.0
## ✔ tidyr 1.3.0 ✔ stringr 1.5.0
## ✔ readr 2.1.3 ✔ forcats 1.0.0
## ── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::between() masks data.table::between()
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::first() masks data.table::first()
## ✖ dplyr::lag() masks stats::lag()
## ✖ dplyr::last() masks data.table::last()
## ✖ purrr::transpose() masks data.table::transpose()</code></pre>
<pre class="r"><code>root_dir &lt;- rprojroot::find_root(rprojroot::has_dir(&quot;.git&quot;))

data_dir &lt;- file.path(root_dir, &quot;data&quot;)
Expand All @@ -477,7 +464,7 @@ <h4 class="date">2023</h4>
<h2>Read in somalier results and histologies files</h2>
<pre class="r"><code>ancestry &lt;- read_tsv(ancestry_file)</code></pre>
<pre><code>## Rows: 1513 Columns: 13
## ── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────
## ── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: &quot;\t&quot;
## chr (2): Kids_First_Biospecimen_ID, predicted_ancestry
## dbl (10): EAS_prob, AFR_prob, AMR_prob, SAS_prob, EUR_prob, PC1, PC2, PC3, P...
Expand All @@ -487,7 +474,7 @@ <h2>Read in somalier results and histologies files</h2>
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.</code></pre>
<pre class="r"><code>hist &lt;- read_tsv(hist_file, guess_max = 1000000)</code></pre>
<pre><code>## Rows: 47633 Columns: 58
## ── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────
## ── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: &quot;\t&quot;
## chr (41): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, a...
## dbl (17): cell_line_passage, OS_days, EFS_days, age_at_diagnosis_days, age_a...
Expand All @@ -500,8 +487,11 @@ <h2>Add data columns from histology file</h2>
<p>demographic data, pathology, and clinical data</p>
<pre class="r"><code># Add participant IDs to `ancestry`
ancestry &lt;- ancestry %&gt;%
left_join(hist[,c(&#39;Kids_First_Biospecimen_ID&#39;, &#39;Kids_First_Participant_ID&#39;, &#39;sample_type&#39;, &quot;cohort_participant_id&quot;)], by = &#39;Kids_First_Biospecimen_ID&#39;) %&gt;%
dplyr::filter(sample_type != &#39;Tumor&#39;)
left_join(hist[,c(&#39;Kids_First_Biospecimen_ID&#39;, &#39;Kids_First_Participant_ID&#39;,
&#39;sample_type&#39;, &quot;cohort_participant_id&quot;,
&#39;reported_gender&#39;, &#39;race&#39;, &#39;ethnicity&#39;)], by = &#39;Kids_First_Biospecimen_ID&#39;) %&gt;%
dplyr::filter(sample_type != &#39;Tumor&#39;,
!grepl(&quot;-P|-M&quot;, cohort_participant_id))

# filter histologies file to exclude Normal samples
hist_tumor &lt;- hist %&gt;%
Expand All @@ -510,8 +500,8 @@ <h2>Add data columns from histology file</h2>

# read in plot_mapping file to add plot group to results
plot_mapping &lt;- read_tsv(plot_mapping_file)</code></pre>
<pre><code>## Rows: 79 Columns: 9
## ── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────
<pre><code>## Rows: 80 Columns: 9
## ── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: &quot;\t&quot;
## chr (8): broad_histology, cancer_group, broad_histology_display, plot_group,...
## dbl (1): broad_histology_order
Expand All @@ -521,16 +511,23 @@ <h2>Add data columns from histology file</h2>
<pre class="r"><code># add histology data to `ancestry` by participant ID
ancestry &lt;- ancestry %&gt;%
dplyr::left_join(hist_tumor[, c(&#39;Kids_First_Participant_ID&#39;, &#39;Kids_First_Biospecimen_ID_tumor&#39;, &#39;sample_id&#39;,
&#39;reported_gender&#39;, &#39;race&#39;, &#39;ethnicity&#39;, &#39;broad_histology&#39;, &#39;cancer_group&#39;,
&#39;broad_histology&#39;, &#39;cancer_group&#39;,
&#39;molecular_subtype&#39;, &#39;tumor_descriptor&#39;, &quot;CNS_region&quot;, &#39;extent_of_tumor_resection&#39;,
&#39;age_at_diagnosis_days&#39;, &#39;OS_days&#39;, &#39;OS_status&#39;, &#39;EFS_days&#39;, &quot;EFS_event_type&quot;,
&#39;age_at_chemo_start&#39;, &#39;age_at_radiation_start&#39;)],
by = &#39;Kids_First_Participant_ID&#39;) %&gt;%
# There is one sample (BS_M52K86E6) with no matched tumor in OPC v14, but is known to have an oligodendroglioma. We will manually enter braod_histology and cancer_group info
dplyr::mutate(broad_histology = case_when(
Kids_First_Biospecimen_ID == &quot;BS_M52K86E6&quot; ~ &quot;Diffuse astrocytic and oligodendroglial tumor&quot;,
TRUE ~ broad_histology),
cancer_group = case_when(
Kids_First_Biospecimen_ID == &quot;BS_M52K86E6&quot; ~ &quot;Oligodendroglioma&quot;,
TRUE ~ cancer_group)
) %&gt;%
dplyr::left_join(plot_mapping[,c(&#39;broad_histology&#39;, &#39;cancer_group&#39;, &#39;plot_group&#39;)], by = c(&#39;broad_histology&#39;, &#39;cancer_group&#39;))</code></pre>
<pre><code>## Warning in dplyr::left_join(., hist_tumor[, c(&quot;Kids_First_Participant_ID&quot;, : Detected an unexpected many-to-many relationship between `x` and `y`.
## ℹ Row 14 of `x` matches multiple rows in `y`.
## ℹ Row 61 of `y` matches multiple rows in `x`.
## ℹ If a many-to-many relationship is expected, set `relationship = &quot;many-to-many&quot;` to silence this warning.</code></pre>
<pre><code>## Warning in dplyr::left_join(., hist_tumor[, c(&quot;Kids_First_Participant_ID&quot;, : Each row in `x` is expected to match at most 1 row in `y`.
## ℹ Row 14 of `x` matches multiple rows.
## ℹ If multiple matches are expected, set `multiple = &quot;all&quot;` to silence this warning.</code></pre>
<p>To select one normal-tumor pair per patient, select matched tumors in
the following prioritization order: intial CNS tumor, recurrent, other.
There are rare cases of different molecular subtypes being called from
Expand All @@ -549,6 +546,17 @@ <h2>Add data columns from histology file</h2>
<p>Merge data to obtain one row per patient</p>
<pre class="r"><code>ancestry_unique &lt;- initial_tumors %&gt;%
bind_rows(recurrent_tumors, other_tumors)</code></pre>
<p>There is one sample (BS_6Z213H2V) with a matched tumor that is
unassigned to a plot group but has high-confidence schwannoma by
methylation subtyping. We will manually enter schwannoma classification,
and assign any other remaining samples with no plot group to “Other
tumor”</p>
<pre class="r"><code>ancestry_unique &lt;- ancestry_unique %&gt;%
dplyr::mutate(plot_group = case_when(
Kids_First_Biospecimen_ID_tumor == &quot;BS_6Z213H2V&quot; ~ &quot;Schwannoma&quot;,
is.na(plot_group) ~ &quot;Other tumor&quot;,
TRUE ~ plot_group
))</code></pre>
</div>
<div id="write-merged-data-to-file" class="section level1">
<h1>Write merged data to file</h1>
Expand Down
18 changes: 13 additions & 5 deletions analyses/add-histologies/02-summary_stats.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -88,9 +88,13 @@ pc12 <- ancestry %>%
ggplot(aes(x = PC1, y = PC2, fill = predicted_ancestry)) +
geom_point(size=2, shape=23,
show.legend = FALSE) +
scale_fill_manual(values = okabe_palette,
labels=c("AFR (n=155)", "AMR (n=224)", "EAS (n=67)",
"EUR (n=996)", "SAS (n=43)")) +
scale_fill_manual(values = okabe_palette) +
# labels=c(glue::glue("AFR (n={sum(ancestry$predicted_ancestry == 'AFR')})"),
# glue::glue("AMR (n={sum(ancestry$predicted_ancestry == 'AMR')})"),
# glue::glue("EAS (n={sum(ancestry$predicted_ancestry == 'EAS')})"),
# glue::glue("EUR (n={sum(ancestry$predicted_ancestry == 'EUR')})"),
# glue::glue("SAS (n={sum(ancestry$predicted_ancestry == 'SAS')})")
# )) +
theme_Publication()


Expand All @@ -99,8 +103,12 @@ pc34 <- ancestry %>%
geom_point(size=2, shape=23) +
labs(fill = "predicted ancestry") +
scale_fill_manual(values = okabe_palette,
labels=c("AFR (n=155)", "AMR (n=224)", "EAS (n=67)",
"EUR (n=996)", "SAS (n=43)")) +
labels=c(glue::glue("AFR (n={sum(ancestry$predicted_ancestry == 'AFR')})"),
glue::glue("AMR (n={sum(ancestry$predicted_ancestry == 'AMR')})"),
glue::glue("EAS (n={sum(ancestry$predicted_ancestry == 'EAS')})"),
glue::glue("EUR (n={sum(ancestry$predicted_ancestry == 'EUR')})"),
glue::glue("SAS (n={sum(ancestry$predicted_ancestry == 'SAS')})")
)) +
theme_Publication()

ggarrange(pc12, pc34,
Expand Down
3 changes: 2 additions & 1 deletion analyses/add-histologies/input/plot-mapping.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -77,4 +77,5 @@ Metastatic tumors Metastatic secondary tumors Other tumor Other tumor #b5b5b5 Me
Non-CNS tumor Myxoid spindle cell tumor Other tumor Other tumor #b5b5b5 Other tumor #b5b5b5 13 Other tumor
Other tumor Other tumor Other tumor Other tumor #b5b5b5 Other tumor #b5b5b5 13 Other tumor
Tumor of pineal region Pineoblastoma Other tumor Other tumor #b5b5b5 Other tumor #b5b5b5 13 Other tumor
Tumor of cranial and paraspinal nerves Schwannoma Tumor of cranial and paraspinal nerves Schwannoma #ffaa00 Schwannoma #ab7200 10 NF or peripheral nerve tumor
Tumor of cranial and paraspinal nerves Schwannoma Tumor of cranial and paraspinal nerves Schwannoma #ffaa00 Schwannoma #ab7200 10 NF or peripheral nerve tumor
Tumor of cranial and paraspinal nerves Malignant peripheral nerve sheath tumor Tumor of cranial and paraspinal nerves Other tumor #b5b5b5 Other tumor #b5b5b5 13 Other tumor
Binary file modified analyses/add-histologies/plots/ancestry-pcs.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/ancestry-race-ethnicity-alluvial.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/ethnicity_ancestry_ct_enr_heatmap.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/lgg_subtype_by_predicted_ancestry.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/lgg_tumor_location_by_predicted_ancestry.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/lgg_tumor_resection_by_predicted_ancestry.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/low_major_ancestry_heatmap.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/major_predicted_ancestry_hist.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/plot_group_ancestry_ct_enr_heatmap.pdf
View file
Open in desktop
Binary file not shown.
Binary file removed analyses/add-histologies/plots/plot_group_ancestry_enrichment_heatmap.pdf
View file
Open in desktop
Binary file not shown.
Binary file removed analyses/add-histologies/plots/plot_group_by_ancestry.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/predicted_ancestry_counts_by_ethnicity.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/predicted_ancestry_counts_by_race.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/predicted_ancestry_percent_by_ethnicity.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/predicted_ancestry_percent_by_race.pdf
View file
Open in desktop
Binary file not shown.
Binary file modified analyses/add-histologies/plots/race_ancestry_ct_enr_heatmap.pdf
View file
Open in desktop
Binary file not shown.
Loading