index.html and style.css set up the web app, which is hosted by GitHub.
The .js files are modulated as described below:
- fetchExpressionData.js contains the fetchExpressionData() function, which returns the following mRNASeq-associated data from Firebrowse as a 1-D array, where each element of the array is a JSON object containing data for a particular cohort-gene pair of the form:
- cohort
- expression_log2
- gene
- geneID
- protocol
- sample_type
- tcga_participant_barcode
- z-score
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getExpressionDataJSONarray.js contains the function: getExpressionDataJSONarray(). This function calls the fetchExpressionData() function and returns the fetched array described above under the fetchExpressionData.js file.
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getExpressionValuesOnly.js contains the getExpressionValuesOnly() function, which utlizes the fetchExpressionData() function to return a 2-D array, where each element in the first (outer) level of the array is a cohort-gene pair, and each element in the second (inner) level of the array is an expression_log2 value. Information about genes that have missing mRNA-Seq data is also returned. This file will likely not have many uses going forward and the getExpressionDataJSONarray.js file is preferable.
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fetchSigMutationData.js contains the fetchSigMutationData() function, which takes two arguments: cohortQuery and numMutations. Where cohortQuery is a TCGA cancer cohort string, and numMutations is the number of top ranked mutations for the given cohort to return. This fetch then returns the full JSON result from Firebrowse (sorted by rank) with the fields:
- codelen
- cohort
- date
- gene
- longname
- nind
- nmis
- nncd
- nnei
- nnon
- npat
- nsil
- nsite
- nspl
- nstp
- p
- pCL
- pCV
- pFN
- q
- rank
- sample_type
- tool
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getSigMutationArray.js contains the function: getSigMutataionArray(). This function calls the fetchSigMutationData() function and returns an array of the top ranked significantly mutated genes for the given cohort query sorted by rank.
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createHeatmap.js contains the functions for building the gene expression heatmap using the mRNA-Seq data that is returned from getExpressionDataJSONarray().
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docManipulation.js contains the functions for manipulating the HTML Doc via JS. This includes tha ability to add/remove DIV elements, the warning/error message functionality, and a function for varifying the validity of user inputted cancer cohorts.