Commit a867dccb authored by Matus Talcik's avatar Matus Talcik
Browse files

Merge branch 'main' of https://github.com/chromoskein/chromoskein

parents 75d02dba 19db7566

app/src/components/RightPanel/ChromatinViewportConfigurationPanel.tsx

+25 −13
Original line number Diff line number Diff line
@@ -129,7 +129,7 @@ export function ChromatinViewportConfigurationPanel(props: { 
        });



    const densityDataOptions = data.data

        .filter(d => d.type == "sparse-1d-data-text" || d.type == "sparse-1d-data-numerical")

        .filter(d => d.type == "sparse-1d-data-text" || d.type == "sparse-1d-data-numerical" || d.type == 'bed-annotation')

        .map(d => {

            return {

                key: isoDataID.unwrap(d.id),
@@ -355,17 +355,29 @@ export function ChromatinViewportConfigurationPanel(props: { 
    const [isSingleColorCalloutVisible, setIsSingleColorCalloutVisible] = useState<boolean>(false);



    const setColorMappingData = (event: React.FormEvent<IComboBox>, option?: IComboBoxOption) => {

        // if (option) {

        //     const selectedDataId: number = option.key as number;

        console.log('color mapping change', configuration.selectedDatum);

        if (option && configuration.selectedDatum != null) {

            console.log('before', configuration.data[configuration.selectedDatum].mapValues);



        //     updateConfiguration({

        //         ...configuration,

        //         mapValues: {

        //             ...configuration.mapValues,

        //             id: selectedDataId,

        //         },

        //     });

        // }

            const selectedDataId: number = option.key as number;



            const newData = configuration.data;

            newData[configuration.selectedDatum] = {

                ...newData[configuration.selectedDatum],

                colorMappingMode: '1d-density',

                mapValues: {

                    ...newData[configuration.selectedDatum].mapValues,

                    id: selectedDataId,

                }

            };



            updateConfiguration({

                ...configuration,

                data: newData

            });



            console.log('after', configuration.data[configuration.selectedDatum].mapValues)

        }

    };



    const setSasaConfiguration = (sasaConfiguration: { method: "constant" | "generated", probeSize: number, accuracy: number, individual: boolean }) => {
@@ -633,8 +645,8 @@ export function ChromatinViewportConfigurationPanel(props: { 


        {configuration.selectedDatum != null && configuration.data.length > configuration.selectedDatum && (<Slider

            label="Radius"

            min={configuration.data[configuration.selectedDatum].radiusRange.min}

            max={configuration.data[configuration.selectedDatum].radiusRange.max}

            min={0.0}

            max={configuration.data[configuration.selectedDatum].radiusRange.max * 2.0}

            step={(configuration.data[configuration.selectedDatum].radiusRange.max - configuration.data[configuration.selectedDatum].radiusRange.min) / 100.0}

            value={toNumber(configuration.data[configuration.selectedDatum].radius)}

            showValue={false}

app/src/components/viewports/ChromatinViewport.tsx

+62 −3
Original line number Diff line number Diff line
@@ -239,15 +239,20 @@ export function ChromatinViewport(props: { 


        const newColors = new Array(configuration.data.length);

        for (const [configurationDatumIndex, configurationDatum] of configuration.data.entries()) {

            const datum = data.data.find(d => d.id === configurationDatum.id)?.values as Positions3D;

            const datum: Data | undefined = data.data.find(d => d.id === configurationDatum.id);



            if (!datum) {

                continue;

            }

            const datumPositions = datum.values as Positions3D;

            const chromatinPart = viewport.getChromatinPartByDataId(configurationDatumIndex);

            let dataMarkers = null;



            if (!datum || !chromatinPart) {

            if (!datumPositions || !chromatinPart) {

                continue;

            }



            const positions = datum.positions;

            const positions = datumPositions.positions;



            const binsAmount = chromatinPart.getBinsPositions().length;
@@ -302,6 +307,60 @@ export function ChromatinViewport(props: { 


                const colorScale = chroma.scale(['#fcfdfd', '#010a4e']);

                newColors[configurationDatumIndex] = chromatinPart.cacheColorArray(mapScaleToChromatin(chromatinPart, globalSasaValues, colorScale));

            } else if (configurationDatum.colorMappingMode == "1d-density") {

                const data1d: Array<{ chromosome: string, from: number, to: number }> | null = data.data.find(d => d.id == isoDataID.wrap(configurationDatum.mapValues.id))?.values as Sparse1DTextData | Sparse1DNumericData | null;

                

                if (!data1d || !(datum.type == '3d-positions')) {

                    return;

                }



                const datumTyped = datum as BinPositionsData;



                const countPerBin: Array<number> = new Array(binsAmount).fill(0);



                const chromosomeData1d = [...data1d.map(v => {return { ...v }})];

                const res = datumTyped.basePairsResolution;



                const connectivity = datumTyped.values.connectivity;



                if (connectivity) {                    

                    const indexes = [];

                    for(let i = 0; i < connectivity.length; i++) {

                        if (connectivity[i] === 0)

                            indexes.push(i);

                    }



                    for(const [i, offset] of indexes.entries()) {

                        const underChrosome = chromosomeData1d.filter(c => parseInt(c.chromosome) === i + 1);



                        for (const v of underChrosome) {

                            v.from += offset * res; 

                            v.to += offset * res;

                        }

                    }

                }



                for (let binIndex = 0; binIndex < binsAmount; binIndex++) {

                    for (const datum of chromosomeData1d) {

                        if (datum.from <= (binIndex + 1) * res 

                        && datum.to >= binIndex * res) {

                            countPerBin[binIndex] += 1;

                        }

                    }

                }



                const logCountPerBin = countPerBin.map(v => Math.log(v) + 1);

                const colorScale = chroma.scale(['#fcfdfd', '#010a4e']);



                newColors[configurationDatumIndex] = chromatinPart.cacheColorArray(mapScaleToChromatin(chromatinPart, logCountPerBin, colorScale));

            } else if (configurationDatum.colorMappingMode == "linear-order") {

                const colorScale = chroma.scale(['#0d1a29', '#133250', '#1e4c7b', '#3868a7', '#658ac6', '#88a0c9', '#aab6ca', '#d3d6da']);



                const numbers = [...Array(binsAmount).keys()];



                console.log(numbers);



                newColors[configurationDatumIndex] = chromatinPart.cacheColorArray(mapScaleToChromatin(chromatinPart, numbers, colorScale));

            }

        }

libs/graphics/src/shaders/2d/distance_map.wgsl

+8 −5
Original line number Diff line number Diff line
@@ -180,18 +180,21 @@ fn main_fragment( 
    //     finalColor = mix(colors[2], colors[3], (newWeight - 0.66) / 0.33);

    // }



    let colors = array<vec3<f32>, 4>(

    let colors = array<vec3<f32>, 5>(

        vec3<f32>(0.17254901960784313725490196078431, 0.10980392156862745098039215686275, 0.30980392156862745098039215686275),

        vec3<f32>(0.29411764705882352941176470588235, 0.45882352941176470588235294117647, 0.62745098039215686274509803921569),

        vec3<f32>(1.0),

        vec3<f32>(0.4078431372549019607843137254902, 0.4078431372549019607843137254902, 0.31372549019607843137254901960784),

        vec3<f32>(0.15294117647058823529411764705882, 0.15294117647058823529411764705882, 0.0078431372549019607843137254902),

    );

    if (newWeight < 0.50) {

        finalColor = mix(colors[0], colors[1], newWeight / 0.50);

    if (newWeight < 0.25) {

        finalColor = mix(colors[0], colors[1], newWeight / 0.25);

    } else if (newWeight < 0.50) {

        finalColor = mix(colors[1], colors[2], (newWeight - 0.25) / 0.25);

    } else if (newWeight < 0.75) {

        finalColor = mix(colors[1], colors[2], (newWeight - 0.50) / 0.25);

        finalColor = mix(colors[2], colors[3], (newWeight - 0.50) / 0.25);

    } else {

        finalColor = mix(colors[2], colors[3], (newWeight - 0.75) / 0.25);

        finalColor = mix(colors[3], colors[4], (newWeight - 0.75) / 0.25);

    }



    return FragmentOutput(

libs/graphics/src/shaders/postprocess/ssao.wgsl

+1 −1
Original line number Diff line number Diff line
@@ -66,7 +66,7 @@ main(@builtin(global_invocation_id) GlobalInvocationID 
  let TBN = mat3x3<f32>(tangent, bitangent, viewSpaceNormal);



  var occlusion = 0.0;

  let numberOfSamples = 4;

  let numberOfSamples = 32;

  for (var i = 0; i < numberOfSamples; i = i + 1) {

    // get sample position

    var samplePos = TBN * globals.noiseSamples[i].xyz; // from tangent to view-space