Upgrading the package

[vincentvfdg]

• More details for the 'plot_seurat_clustree' function.
• Minor detail : need a roxygen skeleton to check_reduction (seurat)
• Is it normal that there are no function in utils.R?
• More details are needed in the MarkDown report. If the html report is better, than it's ok to leave it as it is.
• When sampling the top 10 genes for each cluster, my dataset has 569 genes for 19 clusters. It should be 190 genes. The problem appear if multiple genes have the same adjusted p-value (0.000000...). For example, my cluster 17 has 35 genes with an equal p-value. We should reconsider another statistics or make a function that randomly pool 10 genes if the function identifies more than 10 genes for a cluster. Some clusters have exactly 10 genes, and their p-values were all different.
• We should consider to include a verbose that says that max_mt and min_mt will be ignored if no organism or no list of mitochondrial genes are provided (worked a bit on it while looking at the SingleCell scripts.)

[vincentvfdg]

• Small detail : we accept "human" and "mouse" as organisms. Is there a way that we can include more terms for these species just like in the anno package? Example : human = "human", "homo sapiens", "hs", "h. sapiens".