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* Initial Cleanup * Refactor static cell info * Changes to fix ATAC bar plot * Revert back to manually breaking displayNames * Fix build errors * Add Active Exps * Sort, better padding * Map key, Initial cleanup * Add optional stimulation to getDisplayName
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,173 @@ | ||
| export type CellName = | ||
| "Myeloid_DCs" | ||
| | "pDCs" | ||
| | "Naive_B" | ||
| | "Mem_B" | ||
| | "Plasmablasts" | ||
| | "Regulatory_T" | ||
| | "Naive_Tregs" | ||
| | "Memory_Tregs" | ||
| | "Effector_CD4pos_T" | ||
| | "Naive_Teffs" | ||
| | "Memory_Teffs" | ||
| | "Th1_precursors" | ||
| | "Th2_precursors" | ||
| | "Th17_precursors" | ||
| | "Follicular_T_Helper" | ||
| | "Naive_CD8_T" | ||
| | "Central_memory_CD8pos_T" | ||
| | "Effector_memory_CD8pos_T" | ||
| | "Gamma_delta_T" | ||
| | "Immature_NK" | ||
| | "Mature_NK" | ||
| | "Memory_NK" | ||
| | "HSC" | ||
| | "MPP" | ||
| | "CMP" | ||
| | "MEP" | ||
| | "Ery" | ||
| | "GMP" | ||
| | "LMPP" | ||
| | "CLP" | ||
| | "CD4Tcell" | ||
| | "NKcell" | ||
| | "Monocytes" | ||
| | "Bulk_B" | ||
| | "CD8pos_T" | ||
| | "pHSC" | ||
| | "LSC" | ||
| | "Blast" | ||
|
|
||
| export type CellDisplayName = | ||
| "Monocyte" | ||
| | "Myeloid dendritic cell" | ||
| | "Plasmacytoid dendritic cell" | ||
| | "Bulk B cell" | ||
| | "Naïve B cell" | ||
| | "Memory B cell" | ||
| | "Plasmablast" | ||
| | "Regulatory CD4+ T cell" | ||
| | "Naïve T regulatory cell" | ||
| | "Memory T regulatory cell" | ||
| | "Effector CD4+ T cell" | ||
| | "Naïve T effector cell" | ||
| | "Memory T effector cell" | ||
| | "Th1 precursor" | ||
| | "Th2 precursor" | ||
| | "Th17 precursor" | ||
| | "T follicular helper cell" | ||
| | "CD8+ T cell" | ||
| | "Naïve CD8+ T cell" | ||
| | "Central memory CD8+ T cell" | ||
| | "Effector memory CD8+ T cell" | ||
| | "Gamma-delta T cell" | ||
| | "Immature NK cell" | ||
| | "Mature NK cell" | ||
| | "Memory NK cell" | ||
| | "Hematopoetic stem cell" | ||
| | "Multipotent progenitor" | ||
| | "Common myeloid progenitor" | ||
| | "Megakaryocyte-erythroid progenitor" | ||
| | "Erythrocyte" | ||
| | "Granulocyte-monocyte progenitors" | ||
| | "Lymphocyte-primed multipotent progenitor" | ||
| | "Common lymphoid progenitor" | ||
| | "CD4+ T cell" | ||
| | "NK cell" | ||
| | "Preleukemic Hematopoetic Stem Cells" | ||
| | "Leukemia Stem Cells" | ||
| | "Leukemic Blast Cells"; | ||
|
|
||
| export type CellQueryValue = | ||
| "Myeloid_DCs-U" | ||
| | "pDCs-U" | ||
| | "Naive_B-U" | ||
| | "Naive_B-S" | ||
| | "Mem_B-U" | ||
| | "Mem_B-S" | ||
| | "Plasmablasts-U" | ||
| | "Regulatory_T-U" | ||
| | "Regulatory_T-S" | ||
| | "Naive_Tregs-U" | ||
| | "Naive_Tregs-S" | ||
| | "Memory_Tregs-U" | ||
| | "Memory_Tregs-S" | ||
| | "Effector_CD4pos_T-U" | ||
| | "Effector_CD4pos_T-S" | ||
| | "Naive_Teffs-U" | ||
| | "Naive_Teffs-S" | ||
| | "Memory_Teffs-U" | ||
| | "Memory_Teffs-S" | ||
| | "Th1_precursors-U" | ||
| | "Th1_precursors-S" | ||
| | "Th2_precursors-U" | ||
| | "Th2_precursors-S" | ||
| | "Th17_precursors-U" | ||
| | "Th17_precursors-S" | ||
| | "Follicular_T_Helper-U" | ||
| | "Follicular_T_Helper-S" | ||
| | "Naive_CD8_T-U" | ||
| | "Naive_CD8_T-S" | ||
| | "Central_memory_CD8pos_T-U" | ||
| | "Central_memory_CD8pos_T-S" | ||
| | "Effector_memory_CD8pos_T-U" | ||
| | "Effector_memory_CD8pos_T-S" | ||
| | "Gamma_delta_T-U" | ||
| | "Gamma_delta_T-S" | ||
| | "Immature_NK-U" | ||
| | "Mature_NK-U" | ||
| | "Mature_NK-S" | ||
| | "Memory_NK-U" | ||
| | "HSC" | ||
| | "CD34_Cord_Blood" | ||
| | "CD34_Bone_Marrow" | ||
| | "MPP" | ||
| | "CMP" | ||
| | "MEP" | ||
| | "Ery" | ||
| | "GMP" | ||
| | "LMPP" | ||
| | "CLP" | ||
| | "CD4Tcell" | ||
| | "NKcell" | ||
| | "Monocytes-U" | ||
| | "Mono" | ||
| | "Monocytes-S" | ||
| | "Bulk_B-U" | ||
| | "Bcell" | ||
| | "Bulk_B-S" | ||
| | "CD8pos_T-U" | ||
| | "CD8Tcell" | ||
| | "CD8pos_T-S" | ||
| | "pHSC" | ||
| | "LSC" | ||
| | "Blast" | ||
|
|
||
| // Static information for each cell | ||
| export type CellTypeStaticInfo = { | ||
| readonly id: CellName; | ||
| readonly displayName: CellDisplayName; | ||
| /** | ||
| * Display name used in the Cell Lineage Tree. Insert '/' to break name onto multiple lines | ||
| */ | ||
| readonly treeDisplayName: string; | ||
| readonly unstimImagePath: string; | ||
| readonly stimImagePath?: string; | ||
| readonly unstimCount: number | ||
| readonly stimCount?: number | ||
| readonly stimulable: boolean; | ||
| readonly queryValues?: { | ||
| readonly unstimulated: { Calderon?: CellQueryValue | CellQueryValue[], Corces?: CellQueryValue | CellQueryValue[] }; | ||
| readonly stimulated?: { Calderon: CellQueryValue | CellQueryValue[] } | ||
| } | ||
| readonly color: string; | ||
| } | ||
|
|
||
| // Dynamic information that changes depending on use case | ||
| export type DynamicCellTypeInfo = { | ||
| selected: boolean; | ||
| stimulated: "S" | "U" | "B"; | ||
| readonly selectable: boolean; | ||
| } | ||
|
|
||
| export type CellLineageTreeState = { [key in CellName]: DynamicCellTypeInfo } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,118 @@ | ||
| import { cellTypeStaticInfo } from "../../common/consts"; | ||
| import { CellDisplayName, CellLineageTreeState, CellName, CellQueryValue, CellTypeStaticInfo } from "./types"; | ||
|
|
||
| export const getCellColor = (cell: CellName | CellQueryValue | CellDisplayName): string => { | ||
| return Object.values(cellTypeStaticInfo).find((x: CellTypeStaticInfo) => x.id === cell || x.displayName === cell || extractQueryValues(x, "B").includes(cell as CellQueryValue))?.color ?? "#000000" | ||
| } | ||
|
|
||
| //In some situations, want to be able to display "stimulated" after. In bar plot, the output is used to get Cell color which would break that | ||
| //In these cases, would be extracting from cell query value where that info exists | ||
| export const getCellDisplayName = (cell: CellName | CellQueryValue, appendStim = false): string => { | ||
| let name = Object.values(cellTypeStaticInfo).find((x: CellTypeStaticInfo) => x.id === cell || extractQueryValues(x, "B").includes(cell as CellQueryValue))?.displayName ?? cell | ||
| if (name === cell) console.log("Unable to find display name for " + cell) | ||
| if (appendStim && cell.slice(-2) == "-S") name += " (stimulated)" | ||
| return name | ||
| } | ||
|
|
||
| /** | ||
| * | ||
| * @param cell CellTypeInfo | ||
| * @param want "S" | "U" | "B" The query value(s) wanted | ||
| * @returns array of query values | ||
| */ | ||
| export const extractQueryValues = (cell: CellTypeStaticInfo, want: "S" | "U" | "B"): (CellQueryValue[]) => { | ||
| switch (want) { | ||
| case "U": return cell.queryValues?.unstimulated ? [...Object.values(cell.queryValues.unstimulated).flat()] : [] | ||
| case "S": return cell.queryValues?.stimulated ? [...Object.values(cell.queryValues.stimulated).flat()] : [] | ||
| case "B": return (cell.queryValues?.unstimulated ? Object.values(cell.queryValues.unstimulated).flat() : []).concat(cell.queryValues?.stimulated ? (Object.values(cell.queryValues.stimulated).flat()) : []) | ||
| } | ||
| } | ||
|
|
||
| const cellNames: CellName[] = [ | ||
| "Myeloid_DCs", | ||
| "pDCs", | ||
| "Naive_B", | ||
| "Mem_B", | ||
| "Plasmablasts", | ||
| "Regulatory_T", | ||
| "Naive_Tregs", | ||
| "Memory_Tregs", | ||
| "Effector_CD4pos_T", | ||
| "Naive_Teffs", | ||
| "Memory_Teffs", | ||
| "Th1_precursors", | ||
| "Th2_precursors", | ||
| "Th17_precursors", | ||
| "Follicular_T_Helper", | ||
| "Naive_CD8_T", | ||
| "Central_memory_CD8pos_T", | ||
| "Effector_memory_CD8pos_T", | ||
| "Gamma_delta_T", | ||
| "Immature_NK", | ||
| "Mature_NK", | ||
| "Memory_NK", | ||
| "HSC", | ||
| "MPP", | ||
| "CMP", | ||
| "MEP", | ||
| "Ery", | ||
| "GMP", | ||
| "LMPP", | ||
| "CLP", | ||
| "CD4Tcell", | ||
| "NKcell", | ||
| "Monocytes", | ||
| "Bulk_B", | ||
| "CD8pos_T" | ||
| ] | ||
|
|
||
| /** | ||
| * Initial Selected Cells being query values not cell names is convenient right now, but confusing. Consider changing in future to plain names, like {name: cellName, stim: "B" | "U" | "S"} | ||
| * @param initialSelectedCells cells to select initially, needs to match query values like Bulk_B-U (NOT CELL NAMES). | ||
| * @param interactive disables interacting with nodes | ||
| */ | ||
| export const generateCellLineageTreeState = (initialSelectedCells: CellQueryValue[], interactive: boolean): CellLineageTreeState => { | ||
| //Some iCREs are active in celltypes (Ex: Blast) that are not in the tree. Need to handle this case. Ex: EH38E0243977 is active in Blast | ||
| let cellLineageTreeState = {} as CellLineageTreeState | ||
|
|
||
| for (const cellName of cellNames) { | ||
| //Try to find matches in the query values of cellLineageTreeStaticInfo | ||
| const unstimSelected = initialSelectedCells.some(cell => extractQueryValues(cellTypeStaticInfo[cellName], "U").includes(cell)) | ||
| const stimSelected = initialSelectedCells.some(cell => extractQueryValues(cellTypeStaticInfo[cellName], "S").includes(cell)) | ||
| cellLineageTreeState[cellName] = { | ||
| selected: unstimSelected || stimSelected, | ||
| selectable: interactive, | ||
| stimulated: | ||
| (unstimSelected && stimSelected) ? "B" : | ||
| (unstimSelected && !stimSelected) ? "U" : | ||
| (!unstimSelected && stimSelected) ? "S" : | ||
| "U" | ||
| } | ||
| } | ||
|
|
||
| return cellLineageTreeState | ||
| } | ||
|
|
||
| const svgData = (_svg): string => { | ||
| let svg = _svg.cloneNode(true); | ||
| svg.setAttribute('xmlns', 'http://www.w3.org/2000/svg'); | ||
| let preface = '<?xml version="1.0" standalone="no"?>'; | ||
| return preface + svg.outerHTML.replace(/\n/g, '').replace(/[ ]{8}/g, ''); | ||
| }; | ||
|
|
||
| const downloadData = (text: string, filename: string, type: string = 'text/plain') => { | ||
| const a = document.createElement('a'); | ||
| document.body.appendChild(a); | ||
| a.setAttribute('style', 'display: none'); | ||
| const blob = new Blob([text], { type }); | ||
| const url = window.URL.createObjectURL(blob); | ||
| a.href = url; | ||
| a.download = filename; | ||
| a.click(); | ||
| window.URL.revokeObjectURL(url); | ||
| a.remove(); | ||
| }; | ||
|
|
||
| export const downloadSVG = (ref: React.MutableRefObject<SVGSVGElement>, filename: string) => { | ||
| ref.current && downloadData(svgData(ref.current!), filename, 'image/svg;charset=utf-8'); | ||
| } |
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