Fix log scale breaking box plot in plots tab (#5079)

* fix log scale breaking box plot * update screenshots --------- Co-authored-by: Bryan Lai <[email protected]>
cBioPortal · Jan 7, 2025 · 6376681 · 6376681
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diff --git a/...nce/enrichments_tab_coadread_tcga_pub_mrna_profile_element_chrome_1600x1000.png b/...nce/enrichments_tab_coadread_tcga_pub_mrna_profile_element_chrome_1600x1000.png
diff --git a/...cluding_unprofiled_samples_comparison_tab_clinical_element_chrome_1600x1000.png b/...cluding_unprofiled_samples_comparison_tab_clinical_element_chrome_1600x1000.png
diff --git a/...unprofiled_samples_comparison_tab_mrna_enrichments_element_chrome_1600x1000.png b/...unprofiled_samples_comparison_tab_mrna_enrichments_element_chrome_1600x1000.png
diff --git a/...s/reference/excluding_unprofiled_samples_plots_tab_element_chrome_1600x1000.png b/...s/reference/excluding_unprofiled_samples_plots_tab_element_chrome_1600x1000.png
diff --git a/...ab_include_overlapping_samples_kruskal_wallis_test_element_chrome_1600x1000.png b/...ab_include_overlapping_samples_kruskal_wallis_test_element_chrome_1600x1000.png
diff --git a/...n_page_clinical_tab_log_scale__kruskal_wallis_test_element_chrome_1600x1000.png b/...n_page_clinical_tab_log_scale__kruskal_wallis_test_element_chrome_1600x1000.png
diff --git a/..._page_clinical_tab_swaped_axes_kruskal_wallis_test_element_chrome_1600x1000.png b/..._page_clinical_tab_swaped_axes_kruskal_wallis_test_element_chrome_1600x1000.png
diff --git a/...on_page_methylation_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...on_page_methylation_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...arison_page_methylation_enrichments_tab_two_groups_element_chrome_1600x1000.png b/...arison_page_methylation_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...omparison_page_mrna_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...omparison_page_mrna_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...up_comparison_page_mrna_enrichments_tab_two_groups_element_chrome_1600x1000.png b/...up_comparison_page_mrna_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...arison_page_protein_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...arison_page_protein_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...comparison_page_protein_enrichments_tab_two_groups_element_chrome_1600x1000.png b/...comparison_page_protein_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...ference/no_session_comparison_tab_mrna_enrichments_element_chrome_1600x1000.png b/...ference/no_session_comparison_tab_mrna_enrichments_element_chrome_1600x1000.png
diff --git a/.../remote/screenshots/reference/no_session_plots_tab_element_chrome_1600x1000.png b/.../remote/screenshots/reference/no_session_plots_tab_element_chrome_1600x1000.png
diff --git a/...ference/plots_tab_box_plot_color_by_mutation_count_element_chrome_1600x1000.png b/...ference/plots_tab_box_plot_color_by_mutation_count_element_chrome_1600x1000.png
diff --git a/...ots_tab_box_plot_color_by_mutation_count_log_scale_element_chrome_1600x1000.png b/...ots_tab_box_plot_color_by_mutation_count_log_scale_element_chrome_1600x1000.png
diff --git a/...s/reference/plots_tab_box_plot_color_by_tumor_type_element_chrome_1600x1000.png b/...s/reference/plots_tab_box_plot_color_by_tumor_type_element_chrome_1600x1000.png
diff --git a/..._box_plot_color_by_tumor_type_highlight_categories_element_chrome_1600x1000.png b/..._box_plot_color_by_tumor_type_highlight_categories_element_chrome_1600x1000.png
diff --git a/...nshots/reference/plots_tab_box_plot_log_scale_zero_element_chrome_1600x1000.png b/...nshots/reference/plots_tab_box_plot_log_scale_zero_element_chrome_1600x1000.png
diff --git a/...s/reference/plots_tab_clinical_vs_clinical_boxplot_element_chrome_1600x1000.png b/...s/reference/plots_tab_clinical_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/.../reference/plots_tab_clinical_vs_molecular_boxplot_element_chrome_1600x1000.png b/.../reference/plots_tab_clinical_vs_molecular_boxplot_element_chrome_1600x1000.png
diff --git a/...molecular_vs_clinical_boxplot,_mutation_search_off_element_chrome_1600x1000.png b/...molecular_vs_clinical_boxplot,_mutation_search_off_element_chrome_1600x1000.png
diff --git a/...screenshots/reference/plots_tab_mutation_type_view_element_chrome_1600x1000.png b/...screenshots/reference/plots_tab_mutation_type_view_element_chrome_1600x1000.png
diff --git a/...lots_tab_mutations_driver_mode_vs_clinical_boxplot_element_chrome_1600x1000.png b/...lots_tab_mutations_driver_mode_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...erence/plots_tab_mutations_profile_with_duplicates_element_chrome_1600x1000.png b/...erence/plots_tab_mutations_profile_with_duplicates_element_chrome_1600x1000.png
diff --git a/.../reference/plots_tab_mutations_vs_clinical_boxplot_element_chrome_1600x1000.png b/.../reference/plots_tab_mutations_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...s_tab_mutations_wild_type_mode_vs_clinical_boxplot_element_chrome_1600x1000.png b/...s_tab_mutations_wild_type_mode_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...nce/plots_tab_one_box_clinical_vs_clinical_boxplot_element_chrome_1600x1000.png b/...nce/plots_tab_one_box_clinical_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...tab_search_case_id_in_clinical_vs_clinical_boxplot_element_chrome_1600x1000.png b/...tab_search_case_id_in_clinical_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...ference/plots_tab_with_structural_variant_coloring_element_chrome_1600x1000.png b/...ference/plots_tab_with_structural_variant_coloring_element_chrome_1600x1000.png
diff --git a/...ab_include_overlapping_samples_kruskal_wallis_test_element_chrome_1600x1000.png b/...ab_include_overlapping_samples_kruskal_wallis_test_element_chrome_1600x1000.png
diff --git a/...on_tab_clinical_tab_log_scale__kruskal_wallis_test_element_chrome_1600x1000.png b/...on_tab_clinical_tab_log_scale__kruskal_wallis_test_element_chrome_1600x1000.png
diff --git a/...n_tab_clinical_tab_swaped_axes_kruskal_wallis_test_element_chrome_1600x1000.png b/...n_tab_clinical_tab_swaped_axes_kruskal_wallis_test_element_chrome_1600x1000.png
diff --git a/...son_tab_methylation_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...son_tab_methylation_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...comparison_tab_mrna_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...comparison_tab_mrna_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...iew_comparison_tab_mrna_enrichments_tab_two_groups_element_chrome_1600x1000.png b/...iew_comparison_tab_mrna_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...parison_tab_protein_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...parison_tab_protein_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/..._comparison_tab_protein_enrichments_tab_two_groups_element_chrome_1600x1000.png b/..._comparison_tab_protein_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/.../reference/session_comparison_tab_mrna_enrichments_element_chrome_1600x1000.png b/.../reference/session_comparison_tab_mrna_enrichments_element_chrome_1600x1000.png
diff --git a/...est/remote/screenshots/reference/session_plots_tab_element_chrome_1600x1000.png b/...est/remote/screenshots/reference/session_plots_tab_element_chrome_1600x1000.png
diff --git a/end-to-end-test/remote/specs/core/plots.screenshot.spec.js b/end-to-end-test/remote/specs/core/plots.screenshot.spec.js
@@ -484,6 +484,13 @@ describe('plots tab screenshot tests', function() {
             `${CBIOPORTAL_URL}/results/plots?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=prad_mich&case_set_id=prad_mich_cna&data_priority=0&gene_list=ERG&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=prad_mich_cna&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=prad_mich_mutations&genetic_profile_ids_PROFILE_STRUCTURAL_VARIANT=prad_mich_fusion&plots_coloring_selection=%7B"colorByCopyNumber"%3A"true"%2C"colorBySv"%3A"true"%7D&plots_horz_selection=%7B"dataType"%3A"clinical_attribute"%7D&plots_vert_selection=%7B"selectedGeneOption"%3A2078%2C"dataType"%3A"COPY_NUMBER_ALTERATION"%7D&profileFilter=0&tab_index=tab_visualize`
         );
 
+        await waitForAndCheckPlotsTab();
+    });
+    it('plots tab box plot log scale zero', async () => {
+        await goToUrlAndSetLocalStorage(
+            `${CBIOPORTAL_URL}/results/plots?cancer_study_list=msk_spectrum_tme_2022&tab_index=tab_visualize&case_set_id=msk_spectrum_tme_2022_all&Action=Submit&gene_list=EGFR&plots_horz_selection=%7B"dataType"%3A"clinical_attribute"%2C"selectedDataSourceOption"%3A"METASTATIC_SITE"%2C"selectedGeneOption"%3A1956%2C"selectedGenericAssayOption"%3A"T_cell"%2C"mutationCountBy"%3A"MutationType"%2C"logScale"%3A"false"%7D&plots_vert_selection=%7B"selectedGeneOption"%3A1956%2C"dataType"%3A"SINGLE_CELL_RELATIVE_CELL_TYPE_COUNTS"%2C"logScale"%3A"true"%2C"selectedDataSourceOption"%3A"cell_type_relative_counts"%2C"mutationCountBy"%3A"MutationType"%2C"selectedGenericAssayOption"%3A"T_cell"%7D&plots_coloring_selection=%7B"selectedOption"%3A"-10000_undefined"%7D`
+        );
+
         await waitForAndCheckPlotsTab();
     });
 });

diff --git a/src/shared/components/plots/BoxScatterPlot.tsx b/src/shared/components/plots/BoxScatterPlot.tsx
@@ -563,6 +563,7 @@ export default class BoxScatterPlot<
                 }}
                 orientation="bottom"
                 offsetY={50}
+                domain={this.plotDomain.x}
                 crossAxis={false}
                 label={this.props.axisLabelX}
                 tickValues={
@@ -632,6 +633,7 @@ export default class BoxScatterPlot<
             <VictoryAxis
                 orientation="left"
                 offsetX={50}
+                domain={this.plotDomain.y}
                 crossAxis={false}
                 label={this.yAxisLabel}
                 dependentAxis={true}
@@ -809,7 +811,6 @@ export default class BoxScatterPlot<
                             height={this.chartHeight}
                             standalone={false}
                             domainPadding={this.chartDomainPadding}
-                            domain={this.plotDomain}
                             singleQuadrantDomainPadding={{
                                 [this.dataAxis]: !!this.props
                                     .startDataAxisAtZero,