.. _LabelTransfer_batch1_label:

5. LabelTransfer batch1
=======================
.. code:: r

    suppressPackageStartupMessages({
    library(reticulate)
    library(Seurat)
    library(dplyr)
    library(ggpubr)
    library(sceasy)
    library(future)
    })
    
    # utilities
    
    o<- function(w,h) options(repr.plot.width=w, repr.plot.height=h)
    
    manycolors=c('#e6194b', '#3cb44b', '#ffe119', '#4363d8', '#f58231', 
                 '#911eb4', '#46f0f0', '#f032e6', '#bcf60c', '#fabebe', 
                 '#008080', '#e6beff', '#9a6324', '#fffac8', '#800000', 
                 '#aaffc3', '#808000', '#ffd8b1', '#000075', '#808080',
                 '#4f34ff', '#f340F0')
    
    
    covid.color.table= c(
        'B'="#FFF3B0", 'Plasma'='#E09F3E',
        'T'='#2F6D9D',
        'T CD4'='#68BDDF',
        'T CD8'='#FF046E',
        'CD8 cytotoxic T'='#9D2A2B',
        'T cycling'='#ADA7FF',
        'Treg'='#493A9D',
        'NKT'='#3300FF',
        'NK'='#D543FF',
        'gdT'='#6A24FF',
        'Neu'='#312697',
        'macrophage'='#429783',
        'Mast'='#FF6B3E',
        'cDC1'='#FF8F39',
        'cDC2'='#E7FF3F',
        'moDC'='#FFBCE1',
        'pDC'='#FF72DB',
        'DC'='#FF0022',
        'Mye'='#19C3BE'  
    )
    
    heca.color.table=c(
        'B cell'='#FFF3B0',
        'CD8 T cell'='#FF046E',
        'Dendritic cell'='#FF0022',
        'Macrophage'='#429783',
        'Mast cell'='#FF6B3E',
        'Megakaryocyte'='gray',
        'Monocyte'='#429753',
        'Myeloid cell'='#19C3BE',
        'NK cell'='#D543FF',
        'Neutrophilic granunocyte'='#312697',
        'Plasma B cell'='#E09F3E',
        'T cell'='#2F6D9D'
    )

load data
=========

load hECA data
--------------

.. code:: r

    # convert h5ad to rds format so that R can read it
    sceasy::convertFormat('./lungimm_heca.h5ad', from="anndata", to="seurat",
                           outFile='lungimm_heca.rds')


.. parsed-literal::

    X -> counts
    
    Warning message:
    “Keys should be one or more alphanumeric characters followed by an underscore, setting key from DMAPharmony_bydonor_ to DMAPharmonybydonor_”
    Warning message:
    “All keys should be one or more alphanumeric characters followed by an underscore '_', setting key to DMAPharmonybydonor_”
    Warning message:
    “Keys should be one or more alphanumeric characters followed by an underscore, setting key from PCAharmony_bydonor_ to PCAharmonybydonor_”
    Warning message:
    “All keys should be one or more alphanumeric characters followed by an underscore '_', setting key to PCAharmonybydonor_”



.. parsed-literal::

    An object of class Seurat 
    20492 features across 53299 samples within 1 assay 
    Active assay: RNA (20492 features, 0 variable features)
     6 dimensional reductions calculated: densmap, densmap_harmonyByDonor, dmap_harmony_bydonor, pca, pca_harmony_bydonor, umap


.. code:: r

    # read saved hECA data
    heca = readRDS('./lungimm_heca.rds')

.. code:: r

    # create a clean seurat object
    heca.full = CreateSeuratObject(heca@assays$RNA@data, meta.data = heca@meta.data)
    heca.full@assays$RNA@data <- heca.full@assays$RNA@counts
    heca.full[["umap"]] <- CreateDimReducObject(heca@reductions$umap@cell.embeddings, key = "umap_")


.. parsed-literal::

    Warning message:
    “No assay specified, setting assay as RNA by default.”


.. code:: r

    # show different batches
    o(15,5)
    DimPlot(heca.full, group.by='ann',cols = heca.color.table, split.by = 'study_id', pt.size=0.01, label=T, repel=T)
    
    # print study_id
    unique(heca.full@meta.data$study_id)



.. raw:: html

    <style>
    .list-inline {list-style: none; margin:0; padding: 0}
    .list-inline>li {display: inline-block}
    .list-inline>li:not(:last-child)::after {content: "\00b7"; padding: 0 .5ex}
    </style>
    <ol class=list-inline><li>10.1038/s41591-019-0468-5</li><li>10.1186/s13059-019-1906-x</li><li>10.1038/s41586-020-2157-4</li></ol>
    
    <details>
    	<summary style=display:list-item;cursor:pointer>
    		<strong>Levels</strong>:
    	</summary>
    	<style>
    	.list-inline {list-style: none; margin:0; padding: 0}
    	.list-inline>li {display: inline-block}
    	.list-inline>li:not(:last-child)::after {content: "\00b7"; padding: 0 .5ex}
    	</style>
    	<ol class=list-inline><li>'10.1038/s41586-020-2157-4'</li><li>'10.1038/s41591-019-0468-5'</li><li>'10.1186/s13059-019-1906-x'</li></ol>
    </details>



.. image:: output_6_1.png
   :width: 900px
   :height: 300px


.. code:: r

    heca1 = subset(heca.full, study_id=='10.1038/s41586-020-2157-4')

.. code:: r

    #heca2 = subset(heca.full, study_id=='10.1186/s13059-019-1906-x')

load COVID data
---------------

.. code:: r

    load("./nCoV.integrated.annotated.rda")

.. code:: r

    o(9,8)
    DimPlot(immune.combined, group.by='persample_ann', label=T, repel=T, cols=covid.color.table) + ggtitle(
        "COVID19 lung immune cells")&
    theme(axis.title = element_blank(),
          axis.text = element_blank(), 
          axis.ticks=element_blank())
    
    cairo_pdf(filename = 'covid19.umap.pdf', width = 9,height = 8)
    DimPlot(immune.combined, group.by='persample_ann', label=T, repel=T, cols=covid.color.table) + ggtitle(
        "COVID19 lung immune cells")&
    theme(axis.title = element_blank(),
          axis.text = element_blank(), 
          axis.ticks=element_blank())
    dev.off()



.. raw:: html

    <strong>png:</strong> 2



.. image:: output_11_1.png
   :width: 540px
   :height: 480px


batch-1 label transfer
======================

.. code:: r

    # find genes for label transfer
    DefaultAssay(heca1)<-'RNA'
    heca1 = FindVariableFeatures(heca1, selection.method="vst", nfeatures=2000, verbose=F)
    
    DefaultAssay(immune.combined)<-'RNA'
    immune.combined = FindVariableFeatures(immune.combined, selection.method="vst", nfeatures=2000, verbose=F)

.. code:: r

    #mask horizontal genes
    x=heca1
    masked.genes<-c(
        c(grep("^RPL", rownames(x), value = T),grep("^RPS", rownames(x), value = T)),
    
        grep("^MT-", rownames(x), value = T),
    
        c(grep("^IFI", rownames(x), value = T),grep("^ISG", rownames(x), value = T)),
    
        grep("^SMC[0-9]*", rownames(x), value = T),
    
        grep("^MCM[0-9]*", rownames(x), value = T),
    
        c(grep("^TUBA", rownames(x), value = T),
          grep("^TUBB", rownames(x), value = T),
          grep("^TUBD[0-9]", rownames(x), value = T),
          grep("^TUBE[0-9]", rownames(x), value = T),
          grep("^TUBG[0-9]", rownames(x), value = T)
        ),
    
        c(Seurat::cc.genes.updated.2019$s.genes,
          Seurat::cc.genes.updated.2019$g2m.genes
        ),
    
        c("H1-0","H1-1","H1-10","H1-12P","H1-2","H1-3","H1-4","H1-5","H1-6","H1-7","H1-8",
        "H1-9P","H2AB1","H2AB2","H2AB3","H2AC1","H2AC10P","H2AC11","H2AC12","H2AC13","H2AC14",
        "H2AC15","H2AC16","H2AC17","H2AC18","H2AC19","H2AC20","H2AC21","H2AC2P","H2AC3P","H2AC4",
        "H2AC5P","H2AC6","H2AC7","H2AC8","H2AC9P","H2AJ","H2AL1MP","H2AL1Q","H2AL3",
        "H2AP","H2AQ1P","H2AW","H2AX","H2AZ1","H2AZ2","MACROH2A1","MACROH2A2","H2BC1","H2BC10",
        "H2BC11","H2BC12","H2BC13","H2BC14","H2BC15","H2BC16P","H2BC17","H2BC18",
        "H2BC19P","H2BC20P","H2BC21","H2BC2P","H2BC3","H2BC4","H2BC5","H2BC6","H2BC7","H2BC8",
        "H2BC9","H2BK1","H2BL1P","H2BN1","H2BC12L","H2BU1","H2BU2P","H2BW1","H2BW2",
        "H2BW3P","H2BW4P","H3-7","H3-3A","H3-3B","H3-4","H3-5","H3C1","H3C10","H3C11","H3C12",
        "H3C13","H3C14","H3C15","H3C2","H3C3","H3C4","H3C5P","H3C6","H3C7","H3C8",
        "H3C9P","H3Y1","H3Y2","CENPA","H4-16","H4C1","H4C10P","H4C11","H4C12","H4C13","H4C14",
        "H4C15","H4C2","H4C3","H4C4","H4C5","H4C6","H4C7","H4C8","H4C9"),
        grep("^HIST", rownames(x), value=T)
    )
    
    goi1 = setdiff( VariableFeatures(heca1), masked.genes)
    
    # mask horizontal genes
    x=immune.combined
    masked.genes<-c(
        c(grep("^RPL", rownames(x), value = T),grep("^RPS", rownames(x), value = T)),
    
        grep("^MT-", rownames(x), value = T),
    
        c(grep("^IFI", rownames(x), value = T),grep("^ISG", rownames(x), value = T)),
    
        grep("^SMC[0-9]*", rownames(x), value = T),
    
        grep("^MCM[0-9]*", rownames(x), value = T),
    
        c(grep("^TUBA", rownames(x), value = T),
          grep("^TUBB", rownames(x), value = T),
          grep("^TUBD[0-9]", rownames(x), value = T),
          grep("^TUBE[0-9]", rownames(x), value = T),
          grep("^TUBG[0-9]", rownames(x), value = T)
        ),
    
        c(Seurat::cc.genes.updated.2019$s.genes,
          Seurat::cc.genes.updated.2019$g2m.genes
        ),
    
        c("H1-0","H1-1","H1-10","H1-12P","H1-2","H1-3","H1-4","H1-5","H1-6","H1-7","H1-8",
        "H1-9P","H2AB1","H2AB2","H2AB3","H2AC1","H2AC10P","H2AC11","H2AC12","H2AC13","H2AC14",
        "H2AC15","H2AC16","H2AC17","H2AC18","H2AC19","H2AC20","H2AC21","H2AC2P","H2AC3P","H2AC4",
        "H2AC5P","H2AC6","H2AC7","H2AC8","H2AC9P","H2AJ","H2AL1MP","H2AL1Q","H2AL3",
        "H2AP","H2AQ1P","H2AW","H2AX","H2AZ1","H2AZ2","MACROH2A1","MACROH2A2","H2BC1","H2BC10",
        "H2BC11","H2BC12","H2BC13","H2BC14","H2BC15","H2BC16P","H2BC17","H2BC18",
        "H2BC19P","H2BC20P","H2BC21","H2BC2P","H2BC3","H2BC4","H2BC5","H2BC6","H2BC7","H2BC8",
        "H2BC9","H2BK1","H2BL1P","H2BN1","H2BC12L","H2BU1","H2BU2P","H2BW1","H2BW2",
        "H2BW3P","H2BW4P","H3-7","H3-3A","H3-3B","H3-4","H3-5","H3C1","H3C10","H3C11","H3C12",
        "H3C13","H3C14","H3C15","H3C2","H3C3","H3C4","H3C5P","H3C6","H3C7","H3C8",
        "H3C9P","H3Y1","H3Y2","CENPA","H4-16","H4C1","H4C10P","H4C11","H4C12","H4C13","H4C14",
        "H4C15","H4C2","H4C3","H4C4","H4C5","H4C6","H4C7","H4C8","H4C9"),
        grep("^HIST", rownames(x), value=T)
    )
    
    goi2 = setdiff( VariableFeatures(immune.combined), masked.genes)

.. code:: r

    goi= unique(c(goi1,goi2))
    length(goi)



.. raw:: html

    3254


.. code:: r

    plan("sequential")
    options(future.globals.maxSize = 1000 * 1024^2*4)
    plan("multiprocess", workers = 14)
    
    heca1           <- ScaleData(heca1,           features = goi)
    immune.combined <- ScaleData(immune.combined, features = goi)
    
    plan("sequential")


.. parsed-literal::

    Warning message:
    “Strategy 'multiprocess' is deprecated in future (>= 1.20.0). Instead, explicitly specify either 'multisession' or 'multicore'. In the current R session, 'multiprocess' equals 'multicore'.”
    Centering and scaling data matrix
    
    Centering and scaling data matrix
    


.. code:: r

    plan("sequential")
    options(future.globals.maxSize = 1000 * 1024^2*4)
    plan("multiprocess", workers = 14)
    
    transfer.anchors <- FindTransferAnchors(reference = heca1, query = immune.combined,
                                            dims = 1:30, features=goi)
    plan("sequential")


.. parsed-literal::

    Warning message:
    “207 features of the features specified were not present in both the reference query assays. 
    Continuing with remaining 3047 features.”
    Performing PCA on the provided reference using 3047 features as input.
    
    Projecting cell embeddings
    
    Finding neighborhoods
    
    Finding anchors
    
    	Found 5294 anchors
    
    Filtering anchors
    
    	Retained 1927 anchors
    


.. code:: r

    predictions <- TransferData(anchorset = transfer.anchors, refdata = heca1$ann,
                                dims = 1:30)
    immune.combined <- AddMetaData(immune.combined, metadata = predictions)


.. parsed-literal::

    Finding integration vectors
    
    Finding integration vector weights
    
    Predicting cell labels
    


.. code:: r

    o(10,8)
    DimPlot(immune.combined, group.by='predicted.id', label=T, repel=T, cols=heca.color.table, order='Neutrophilic granunocyte')
    DimPlot(immune.combined, group.by='persample_ann', label=T, repel=T, cols=covid.color.table)



.. image:: output_19_0.png
   :width: 600px
   :height: 480px



.. image:: output_19_1.png
   :width: 600px
   :height: 480px


.. code:: r

    o(10,8)
    DimPlot(immune.combined, group.by='predicted.id', label=T, repel=T, cols=heca.color.table)
    DimPlot(immune.combined, group.by='persample_ann', label=T, repel=T, cols=covid.color.table)



.. image:: output_20_0.png
   :width: 600px
   :height: 480px



.. image:: output_20_1.png
   :width: 600px
   :height: 480px


.. code:: r

    matched <- c(
        paste('B' , 'B cell', sep="_"),
        paste('Plasma' , 'Plasma B cell', sep="_"),
        paste('Plasma' , 'B cell', sep="_"),
        paste('T' , 'CD8 T cell', sep="_"),
        paste('T' , 'T cell', sep="_"),
        paste('T CD4' , 'T cell', sep="_"),
        paste('T CD8' , 'T cell', sep="_"),
        paste('T CD8' , 'CD8 T cell', sep="_"),
        paste('CD8 cytotoxic T' , 'T cell', sep="_"),
        paste('CD8 cytotoxic T' , 'CD8 T cell', sep="_"),
        paste('T cycling' , 'T cell', sep="_"),
        paste('T cycling' , 'CD8 T cell', sep="_"),    
        paste('Treg' , 'T cell', sep="_"),
        paste('gdT' , 'T cell', sep="_"),
        paste('NKT' , 'T cell', sep="_"),
        paste('NK' , 'NK cell', sep="_"),
        paste('Neu' , 'Neutrophilic granulocyte', sep="_"),
        paste('macrophage' , 'Macrophage', sep="_"),
        paste('macrophage' , 'Monocyte', sep="_"),
        paste('macrophage' , 'Myeloid cell', sep="_"),
    
        paste('Mast' , 'Mast cell', sep="_"),
        paste('cDC1' , 'Dendritic cell', sep="_"),
        paste('cDC1' , 'Myeloid cell', sep="_"),
        paste('cDC2' , 'Dendritic cell', sep="_"),
        paste('cDC2' , 'Myeloid cell', sep="_"),
        paste('moDC' , 'Dendritic cell', sep="_"),
        paste('pDC' , 'Dendritic cell', sep="_"),
        paste('DC'  , 'Dendritic cell', sep="_"),
        paste('Mye' , 'Macrophage', sep="_"),
        paste('Mye' , 'Mast cell', sep="_"),
        paste('Mye' , 'Megakaryocyte', sep="_"),
        paste('Mye' , 'Dendritic cell', sep="_"),
        paste('Mye' , 'Monocyte', sep="_"),
        paste('Mye' , 'Neutrophilic granulocyte', sep="_"),
        paste('Mye' , 'Myeloid cell', sep="_")
    )

.. code:: r

    # calculate accuracy
    meta=immune.combined@meta.data
    meta = meta[, c('persample_ann','predicted.id')]
    meta$joint <- paste(meta$persample_ann, meta$predicted.id, sep='_')
    meta$isMatched <- (meta$joint %in% matched) | (meta$persample_ann == meta$predicted.id)
    acc = (meta %>% filter(isMatched==T) %>% nrow) / (meta %>% nrow)
    print( acc )


.. parsed-literal::

    [1] 0.8283611


.. code:: r

    # draw matrix
    
    ## create an empty adj matrix
    rows = as.character( unique(immune.combined@meta.data$persample_ann) ) # from:covid ground-truth
    cols = as.character( unique(heca.full@meta.data$cell_type) ) # to:predicted to
    mat <- matrix(0, length(rows), length(cols))
    rownames(mat) <- rows
    colnames(mat) <- cols
    
    # get an edge list
    edge.list = meta %>% count(persample_ann, predicted.id, sort = TRUE)
    
    # fill in the edge list
    for(i in 1:NROW(edge.list)) mat[ edge.list[i,1], edge.list[i,2] ] <- edge.list[i,3]  # SEE UPDATE
    
    row.order= c('Plasma','B',
    'Treg','T cycling','T CD4','T','NKT','gdT','CD8 cytotoxic T',
    'T CD8','NK',
    'Neu','DC','cDC2','cDC1','macrophage','moDC','pDC','Mast'
    )
    col.order=c('Plasma B cell','B cell',
    'T cell','CD8 T cell','NK cell',
    'Neutrophilic granulocyte',
    'Macrophage','Dendritic cell','Myeloid cell','Mast cell','Monocyte','Megakaryocyte')
    
    
    # row-sum scaling
    mat = mat/rowSums(mat)
    mat = mat[row.order,col.order]
    library(pheatmap)
    o(5,5)
    pheatmap(mat, cluster_rows = F, cluster_cols = F,main='hECA batch1 reference')



.. image:: output_23_0.png
   :width: 300px
   :height: 300px


.. code:: r

    library('mclust')
    adjustedRandIndex(meta$persample_ann, meta$predicted.id)


.. parsed-literal::

    Package 'mclust' version 5.4.9
    Type 'citation("mclust")' for citing this R package in publications.
    



.. raw:: html

    0.305493881788284