Mostly UI updates#495
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ZhenghaoZhu merged 15 commits intodevelopmentfrom Oct 29, 2024
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- Heatmap itself is still not responsive (a work in progress) - Heatmap no longer extends rightward beyond width of tabs - Updated some aesthetics of heatmap section (font sizes, labels' text) - Updated comments to be more instructive
- Shortened and centered title - Added expression value to y-axis - Updated font sizes
- Heatmap itself is still not responsive (a work in progress) - Heatmap no longer extends rightward beyond width of tabs - Updated some aesthetics of heatmap section (font sizes, labels' text) - Updated comments to be more instructive
- Shortened and centered title - Added expression value to y-axis - Updated font sizes
- Because, previously, these were getting cut off in the visualization
…ta explore section - Previously, many of these clinical features were represented as pie charts, which made the values difficult to read
- It does not contain any patient barcodes/expression data
- Removed 'date' and 'tool' because they yield the same value across all tumor types - Removed 'tcga_participant_barcode' because it does not align with the purpose of the data explore section at the moment
…ck/partition lists for heatmap and violin plots - For same reason as why they were removed from clinical feature select dropdown
This was
linked to
issues
Oct 18, 2024
ZhenghaoZhu
reviewed
Oct 19, 2024
Comment on lines
+338
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| let continuousFeaturesArr = [ | ||
| "age_began_smoking_in_years", | ||
| "age_at_diagnosis", | ||
| "cervix_suv_results", | ||
| "date_of_initial_pathologic_diagnosis", | ||
| "days_to_death", | ||
| "days_to_last_followup", | ||
| "days_to_last_known_alive", | ||
| "days_to_psa", | ||
| "days_to_submitted_specimen_dx", | ||
| "gleason_score", | ||
| "height_cm_at_diagnosis", | ||
| "initial_pathologic_dx_year", | ||
| "karnofsky_performance_score", | ||
| "lymph_nodes_examined", | ||
| "lymph_nodes_examined_he_count", | ||
| "number_of_lymph_nodes", | ||
| "number_pack_years_smoked", | ||
| "pregnancies_count_ectopic", | ||
| "pregnancies_count_live_birth", | ||
| "pregnancies_count_stillbirth", | ||
| "pregnancies_count_total", | ||
| "pregnancy_spontaneous_abortion_count", | ||
| "pregnancy_therapeutic_abortion_count", | ||
| "psa_value", | ||
| "tobacco_smoking_history", | ||
| "tobacco_smoking_pack_years_smoked", | ||
| "tobacco_smoking_year_stopped", | ||
| "weight_kg_at_diagnosis", | ||
| "years_to_birth", | ||
| "year_of_tobacco_smoking_onset" | ||
| ]; // Array of features that should be considered continuous |
Collaborator
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This seems to be a constant which are normally placed in a constants.js file. Furthermore, constant names are capitalized and use snake case. In this case, this would let CONTINUOUS_FEATURES = []. No need to add "arr" as the features key word implies multiple items.
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| para.setAttribute( | ||
| "style", | ||
| 'text-align: center; color: #4db6ac; font-family: Georgia, "Times New Roman", Times, serif' | ||
| ); |
Collaborator
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This is similar to the code above
// build label:
let para = document.createElement("p");
// Style the paragraph
para.style.textAlign = 'center';
para.style.color = '#4db6ac';
para.style.fontFamily = 'Georgia, "Times New Roman", Times, serif';
para.id = "numSamplesInCohortText2";
Instead of doing this, you could create a function to set all of these attributes. This would be useful to make sure all attributes we want to modify are accounted for each time.
| } | ||
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| const unwantedKeys = new Set(['date', 'tcga_participant_barcode', 'tool']); |
Collaborator
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It seems this set variable is declared in multiple places. It would be good practice to have a shared file instead of re-declaring the variable in each file every time.
enemeth19
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ZhenghaoZhu and
adit-anand
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adit-anand
ZhenghaoZhu
approved these changes
Oct 29, 2024
ZhenghaoZhu
pushed a commit
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this pull request
Mar 10, 2025
* - Added responsiveness to heatmap legend - Heatmap itself is still not responsive (a work in progress) - Heatmap no longer extends rightward beyond width of tabs - Updated some aesthetics of heatmap section (font sizes, labels' text) - Updated comments to be more instructive * Update violin plots' formatting - Shortened and centered title - Added expression value to y-axis - Updated font sizes * Add text to display number of samples in final cohort * - Added responsiveness to heatmap legend - Heatmap itself is still not responsive (a work in progress) - Heatmap no longer extends rightward beyond width of tabs - Updated some aesthetics of heatmap section (font sizes, labels' text) - Updated comments to be more instructive * Update violin plots' formatting - Shortened and centered title - Added expression value to y-axis - Updated font sizes * Add text to display number of samples in final cohort * Update min and max values displayed in violin plots - Because, previously, these were getting cut off in the visualization * Decrease top margin of violin plots section * Represent clinical features with numerical values as histograms in data explore section - Previously, many of these clinical features were represented as pie charts, which made the values difficult to read * Remove 'FPPP' from tumor types dropdown - It does not contain any patient barcodes/expression data * DIsable certain options from clinical feature dropdown - Removed 'date' and 'tool' because they yield the same value across all tumor types - Removed 'tcga_participant_barcode' because it does not align with the purpose of the data explore section at the moment * Remove 'date', 'tcga_participant_barcode', and 'tool' from sample track/partition lists for heatmap and violin plots - For same reason as why they were removed from clinical feature select dropdown * Increase font size of heatmap sample track labels * Revise based on Kevin's review
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See commit messages for notes on which features have UI updates