DotPlotCompare.RdDotPlotCompare
DotPlotCompare( new.object = NULL, show = "gene", split.by = "orig.ident", scaling = "log", size = "pct.exp", idents = "all", classification = "DKCC", dot.min = 0.1, dot.scale = 6, col.min = NA, col.max = NA, scale.min = NA, scale.max = NA, scale.by = "radius", features, compare.to.organoids = FALSE, filter.samples = NULL, columns = NULL )
| new.object | seurat object to compare to reference data |
|---|---|
| show | this defines the focus of the output; "gene" partitions by gene, anything else partitions by segment |
| split.by | meta.data column to split the sample by, usually the sample column |
| scaling | choose "log", "scale" or "raw" to change how the expression values are displayed |
| size | how to scale the size of the dot, "pct.exp" for the percent of cells expressing the gene, "Pct" is percent of cells in identity |
| idents | Identities to display. Use "all" to show all segments, "nephron" to show all nephron segments, "others" to show all non-nephron segments, or a string of identities to select specific Identities |
| classification | choose "DKCC" or "LineageID" |
| dot.min | dot size of minimum cell percentage |
| dot.scale | dot size of maximum cell percentage |
| col.min | minimum expression value to plot |
| col.max | maximum expression value to plot |
| scale.min | minimum scale |
| scale.max | maximum scale |
| scale.by | "radius" or "size" |
| features | features to plot |
| compare.to.organoids | if function should plot organoid samples from the database |
| filter.samples | if compare.to.organoids=T, can provide desired sample names here using the output from "GetSampleIDs". |
| columns | how many columns to plot. Default is to plot as square as possible. |
ggplot object