Report improvements

bihealth · Oct 16, 2024 · 3dd881d · 3dd881d
1 parent 1cc5f0a
commit 3dd881d
Show file tree

Hide file tree

Showing 4 changed files with 39 additions and 21 deletions.
diff --git a/stemcnv_check/scripts/R/R_plotting_functions.R b/stemcnv_check/scripts/R/R_plotting_functions.R
@@ -134,7 +134,7 @@ make_LRR_BAF_plots <- function(
         ) +
         scale_x_continuous(
             expand = expansion(),
-            labels = label_number(big.mark = '..', decimal.mark = ','),
+            labels = label_number(big.mark = '.', decimal.mark = ','),
             limits = c(win_start, win_end),
             oob = oob_keep
         ) +
@@ -196,7 +196,7 @@ make_LRR_BAF_plots <- function(
         theme_classic() +
         scale_x_continuous(
             expand = expansion(),
-            labels = label_number(big.mark = '..', decimal.mark = ','),
+            labels = label_number(big.mark = '.', decimal.mark = ','),
             limits = c(win_start, win_end),
             position = 'top'
         ) +
@@ -225,7 +225,7 @@ make_LRR_BAF_plots <- function(
         theme_classic() +
         scale_x_continuous(
             expand = expansion(),
-            labels = label_number(big.mark = '..', decimal.mark = ','),
+            labels = label_number(big.mark = '.', decimal.mark = ','),
             limits = c(win_start, win_end),
             oob = oob_keep
         ) +
@@ -254,7 +254,7 @@ make_LRR_BAF_plots <- function(
         theme_classic() +
         scale_x_continuous(
             expand = expansion(),
-            labels = label_number(big.mark = '..', decimal.mark = ','),
+            labels = label_number(big.mark = '.', decimal.mark = ','),
             limits = c(win_start, win_end),
             oob = oob_keep
         ) +

diff --git a/stemcnv_check/scripts/R/R_table_functions.R b/stemcnv_check/scripts/R/R_table_functions.R
@@ -388,13 +388,13 @@ gene_table_output <- function(
 }
 
 hotspot_table_output <- function(
-    hotspots, plotsection, high_impact_tb, highlight_tb, report_config, out_format, caption = NULL
+    hotspots, cnv_type, plotsection, high_impact_tb, highlight_tb, report_config, out_format, caption = NULL
 ){
     tb <- bind_rows(
         high_impact_tb,
         highlight_tb
     ) %>%
-        filter(hotspot %in% hotspots) 
+        filter(hotspot %in% hotspots & call_type %in% c('any', cnv_type))
 
     if (out_format == 'html') {
         dt <- datatable(

diff --git a/stemcnv_check/scripts/report_template.Rmd b/stemcnv_check/scripts/report_template.Rmd
@@ -193,7 +193,7 @@ make_CNV_plot_section <- function(call.table, plotsection = 'denovo') {
             # message(str_glue('N hotspots: {length(res$hotspots)}'))
             if (report_config$call.data.and.plots[[plotsection]]$include.hotspot.table & length(res$hotspots)>0) {
                 res$hotspots %>%
-                    hotspot_table_output(plotsection, high_impact_tb, highlight_tb, report_config, params$out_format) %>%
+                    hotspot_table_output(plotsection, row$CNV_type, high_impact_tb, highlight_tb, report_config, params$out_format) %>%
                     subchunkify(str_glue('CNV_call.{plotsection}.nr{i}.hotspots'))
                 cat('\n\n')
             }
@@ -266,12 +266,12 @@ repo_excl_filters <- ifelse(
 cat(paste(
     'Call designation takes into account the Check_Score thresholds for critical and optoinally reportable level.',
     'Additionally, calls having an exclusion filter (i.e. below minimum size, or having a probe coverage gap) ',
-    'for a specific designation are assigend the next lower level (i.e. critical -> reportable or reportable -> no label).\n',
-    'The current thresholds and exclsuion filters are:\n',
-    ' - Critical Check_Score:', config$evaluation_settings$CNV_call_categorisation$check_score.critical, '\n',
-    ' - Critical exclusion Filters:', crit_excl_filters, '\n',
-    ' - Reportable Check_Score:', config$evaluation_settings$CNV_call_categorisation$check_score.reportable, '\n',
-    ' - Reportable exclusion Filters: ', repo_excl_filters
+    'for a specific designation are assigend the next lower level (i.e. critical -> reportable or reportable -> no label).\n\n',
+    'The current thresholds and exclsuion filters are:\n\n',
+    ' - Critical Check_Score:', config$evaluation_settings$CNV_call_categorisation$check_score.critical, '\n\n',
+    ' - Critical exclusion Filters:', crit_excl_filters, '\n\n',
+    ' - Reportable Check_Score:', config$evaluation_settings$CNV_call_categorisation$check_score.reportable, '\n\n',
+    ' - Reportable exclusion Filters: ', repo_excl_filters, '\n\n'
 ))
 
 read_excel(
@@ -401,7 +401,10 @@ denovo_calls.table <- cnv_calls %>%
     dplyr::rename(chrom = seqnames, Size = width) %>%
     arrange(desc(Check_Score), desc(Size), chrom, start) %>%
     filter(sample_id == !!sample_id & Call_label != 'Reference genotype') %>%
-    filter(!str_detect(FILTER, denovo_filter_regex)) %>%
+    filter(
+        !str_detect(FILTER, denovo_filter_regex) | 
+            Call_label %in% report_config$call.data.and.plots$denovo$always_include
+    ) %>%
     mutate(i = row_number())
 
 refgt_filter_regex <- ifelse(
@@ -412,7 +415,10 @@ refgt_filter_regex <- ifelse(
 reference_calls.table <- cnv_calls %>% 
     dplyr::rename(chrom = seqnames, Size = width) %>%
     arrange(desc(Check_Score), desc(Size), chrom, start) %>%
-    filter(sample_id == !!sample_id & Call_label == 'Reference genotype') %>%
+    filter(
+        sample_id == !!sample_id & Call_label == 'Reference genotype' |
+            Call_label %in% report_config$call.data.and.plots$reference_gt$always_include
+    ) %>%
     filter(!str_detect(FILTER, refgt_filter_regex)) %>%
     mutate(i = row_number())
 

diff --git a/tests/testthat/test_report_table_functions.R b/tests/testthat/test_report_table_functions.R
@@ -77,9 +77,10 @@ test_that("format_hotspots_to_badge", {
     )
 })
 
-# hotspot_table_output(hotspots, plotsection, high_impact_tb, highlight_tb, report_config, out_format) %>%
+# hotspot_table_output(hotspots, cnv_type, plotsection, high_impact_tb, highlight_tb, report_config, out_format) %>%
 test_that("hotspot_table_output", {
-    hotspots <- c('dummyC', '1p36')
+    hotspots <- c('DDX11L1', '1p36')
+    cnv_type <- 'loss'
     high_impact_tb <- load_hotspot_table(config, 'HighImpact') 
     highlight_tb <- tibble()
     # these aren't used so far
@@ -109,7 +110,7 @@ test_that("hotspot_table_output", {
             escape = FALSE
         )
 
-    hotspot_table_output(hotspots, plotsection, high_impact_tb, highlight_tb, report_config, 'html') %>%
+    hotspot_table_output(hotspots, cnv_type, plotsection, high_impact_tb, highlight_tb, report_config, 'html') %>%
         expect_equal(expected)
 
     # test non-html output
@@ -118,7 +119,7 @@ test_that("hotspot_table_output", {
         dplyr::rename(dois = description_doi) %>%
         rename_with(format_column_names) %>% 
         kable()
-    hotspot_table_output(hotspots, plotsection, high_impact_tb, highlight_tb, report_config, 'not-html') %>%
+    hotspot_table_output(hotspots, cnv_type, plotsection, high_impact_tb, highlight_tb, report_config, 'not-html') %>%
         expect_equal(expected)
 
     # test with highlight table
@@ -133,7 +134,7 @@ test_that("hotspot_table_output", {
         dplyr::rename(dois = description_doi) %>%
         rename_with(format_column_names) %>% 
         kable()
-    hotspot_table_output(hotspots, plotsection, high_impact_tb.no_ov, highlight_tb, report_config, 'not-html') %>%
+    hotspot_table_output(hotspots, cnv_type, plotsection, high_impact_tb.no_ov, highlight_tb, report_config, 'not-html') %>%
         expect_equal(expected)
     # test with same hotspot in both HighImpact and highlight table
     expected <- expected_tb %>% 
@@ -157,6 +158,17 @@ test_that("hotspot_table_output", {
             rownames = FALSE,
             escape = FALSE
         )
-    hotspot_table_output(hotspots, plotsection, high_impact_tb, highlight_tb, report_config, 'html') %>%
+    hotspot_table_output(hotspots, cnv_type, plotsection, high_impact_tb, highlight_tb, report_config, 'html') %>%
         expect_equal(expected)
+    # test with only partially matching cnv_type
+    cnv_type <-  'LOH'
+    expected <- expected_tb %>%
+        filter(hotspot == 'DDX11L1') %>%
+        select(hotspot, call_type, list_name, description, check_score, description_doi) %>%
+        dplyr::rename(dois = description_doi) %>%
+        rename_with(format_column_names) %>% 
+        kable()
+    hotspot_table_output(hotspots, cnv_type, plotsection, high_impact_tb, highlight_tb, report_config, 'not-html') %>%
+        expect_equal(expected)
+
 })