ssion[,cell_name_1]","marks":[]}],"key":"2JWxSZCieGOE"}],"key":"uHHhMBzgTQI1"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" Expression_2 <- h5ad$expression[,cell_name_2]","marks":[]}],"key":"gudI8HtXJc7M"}],"key":"vYis6tJQwPM3"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":"","marks":[]}],"key":"3nntuKKePLTu"}],"key":"5hxYl5g8i5am"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" ## log FC","marks":[]}],"key":"PSxYLUuF0Ytu"}],"key":"4SRANT2axrPm"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" mean_c1 <- as.data.frame(rowMeans(as.matrix(Expression_1)))","marks":[]}],"key":"JeGaEwL3mas4"}],"key":"IQxss8AiVKjK"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" colnames(mean_c1) <- \"mean_c1\"","marks":[]}],"key":"dWvCsJ8uzeMR"}],"key":"FYHmlrrAliHG"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" mean_c2 <- as.data.frame(rowMeans(as.matrix(Expression_2)))","marks":[]}],"key":"AuwJAxwFjP0A"}],"key":"GKS33qzWWr37"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" colnames(mean_c2) <- \"mean_c2\"","marks":[]}],"key":"Zo4T6ZByeDSY"}],"key":"275SNxh9ov8L"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" log2fc <- data.frame(log2fc = log2(mean_c1$mean_c1 + pseudocount.use) - log2(mean_c2$mean_c2 + pseudocount.use))","marks":[]}],"key":"5TYWfZ4DN1zH"}],"key":"DXhjQC4kDzCf"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" rownames(log2fc) <- rownames(mean_c1)","marks":[]}],"key":"nc8xwyfVMxBc"}],"key":"Bnipj6mBeEW2"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" log2fc$gene <- rownames(log2fc)","marks":[]}],"key":"9EKwTWAOvzUu"}],"key":"Z4u8bEPsB6wc"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":"","marks":[]}],"key":"FbprytCGfltb"}],"key":"0ifOd62FoFbl"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" ## wilcox test","marks":[]}],"key":"NiBFansDvDRU"}],"key":"5zDtv9VJzMH3"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" group.info <- data.frame(row.names = c(cell_name_1, cell_name_2))","marks":[]}],"key":"gZHlTa1Jh7UT"}],"key":"hhgtKmAIxmjx"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" group.info[cell_name_1, \"group\"] <- \"Group1\"","marks":[]}],"key":"uVVvEgUJDPSg"}],"key":"HIgbQhqgGlfp"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" group.info[cell_name_2, \"group\"] <- \"Group2\"","marks":[]}],"key":"5RCztFb4gVy5"}],"key":"n80drlUx9s2p"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" group.info[, \"group\"] <- factor(x = group.info[, \"group\"])","marks":[]}],"key":"XZgcoRE5PD8m"}],"key":"0WZKeTuLJGIK"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":" data.use <- h5ad$expression[, rownames(x = group.info), drop = FALSE]","marks":[]}],"key":"n2wQ1JFgP7pS"}],"key":"WFhy1imNjSud"},{"object":"block","type":"code-line","isVoid":false,"data":{},"nodes":[{"object":"text","leaves":[{"object":"leaf","text":""