seurat单细胞数据分析实现 DimHeatmap函数
上游分析:https://www.jianshu.com/p/4f7aeae81ef1
001、
cell <- pbmc[["pca"]]@cell.embeddings cell <- cell[order(cell[,1], decreasing = T),] cell <- rownames(cell)[c(1:10, (length(rownames(cell)) - 9):length(rownames(cell)))] cell ## 提取细胞 feature <- pbmc[["pca"]]@feature.loadings feature <- feature[order(feature[,1], decreasing = T),] feature <- rownames(feature)[c(1:15, (length(rownames(feature)) - 14):length(rownames(feature)))] feature ## 提取基因 dat <- pbmc[["RNA"]]@scale.data dat <- t(dat)[cell, feature] ## 提取绘图数据 par(mar = c(1, 1, 3, 5)) plot.new() image(dat, axes = FALSE,add = TRUE, ## 绘图 col = PurpleAndYellow() ) axis(side = 4, at = seq(0, 1, length = ncol(dat)), labels = colnames(dat), las = 1, tick = FALSE, mgp = c(0, -0.5, 0), cex.axis = 0.75 ) title(main = "PC1")
002、标准答案
DimHeatmap(pbmc, dims = 1, cells = 20, balanced = TRUE)
003、使用默认颜色
par(mar = c(1, 1, 3, 5)) plot.new() image(dat, axes = FALSE,add = TRUE, #col = PurpleAndYellow() ) axis(side = 4, at = seq(0, 1, length = ncol(dat)), labels = colnames(dat), las = 1, tick = FALSE, mgp = c(0, -0.5, 0), cex.axis = 0.75 ) title(main = "PC1")
004、增加细胞名称
par(mar = c(9, 1, 3, 5)) plot.new() image(dat, axes = FALSE,add = TRUE, #col = PurpleAndYellow() ) axis(side = 4, at = seq(0, 1, length = ncol(dat)), labels = colnames(dat), las = 1, tick = FALSE, mgp = c(0, -0.5, 0), cex.axis = 0.75 ) axis(side = 1, at = seq(0, 1, length = nrow(dat)), labels = rownames(dat), ## 增加细胞名称 las = 2, tick = FALSE, mgp = c(0, -0.5, 0), cex.axis = 0.75 ) title(main = "PC1")