I am trying to understand what the correct units are for the violin plots output by Seurat. The Y axis is labeled "Expression Level" by default on their violin plots. If I input a matrix of counts values will my units then be log counts? likewise, if i input a matrix of TPM values will the units be log TPM?
Or alternatively are the units changed by the internal Seurat normalization process? Seurat (v220.127.116.11) has normalization process run using
Setup(object, project, min.cells = 3, min.genes = 1000, is.expr = 0,
do.logNormalize = T, total.expr = 10000, do.scale = TRUE,
do.center = TRUE, names.field = 1, names.delim = "_",
meta.data = NULL, save.raw = TRUE)
Some of the arguments for setup seem to include additional data normalization steps.
do.logNormalize = whether to normalize the expression data per cell and transform to log space.
do.scale = In firstname.lastname@example.org, perform row-scaling (gene-based z-score)
do.center = In email@example.com, perform row-centering (gene-based centering)
What are the appropriate units for data imported in this way?
NOTE: yes i know Seurat (v18.104.22.168) is outdated. But i am trying to understand data that was processed using this version.