Doheatmap in seurat
Hi guys (sorry I cannot show the full heatmap as it is about to be in a paper),
I am trying to reorder this heatmap's identity where instead of BGH>CFAP>NM>WT we have WT>CFAP>NM>BGH.
How do I do that in doheatmap? Here is the code that gave me this order:
c1 <- subset(trac_all_cc, idents = "1")
c1 <- ScaleData(c1, features = NULL, assay = "SCT")
c1_df <- as.data.frame(c1@assays$SCT@scale.data) |> tibble::rownames_to_column() |> filter(rowname %in% top50$gene)
c1_df <- c1_df |> tibble::column_to_rownames() #genes back to rownames
d <- dist(c1_df, method = "euclidean")
hc <- hclust(d, method = "ward.D2")
gene_order <- hc$order
gene_ordernames <- rownames(c1_df)[gene_order]
p <- DoHeatmap(c1, features = gene_ordernames, group.by = "Sample_name")
2 answers
c1$Sample_name <- factor(c1$Sample_name, levels = c("WT", "CFAP", "NM", "BGH"))
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jared.andrews07
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