heatmap.gg.plot {iCellR} | R Documentation |
This function takes an object of class iCellR and genes and provides a heatmap.
heatmap.gg.plot( x = NULL, gene = "NULL", cell.sort = FALSE, data.type = "main", cluster.by = "clusters", conds.to.plot = NULL, min.scale = -2.5, max.scale = 2.5, interactive = TRUE, cex.col = 10, cex.row = 10, no.key = FALSE, out.name = "plot", heat.colors = c("blue", "white", "red") )
x |
A data frame containing gene counts for cells. |
gene |
A set of gene names to be heatmapped. |
cell.sort |
If FALSE the cells will not be sorted based on their distance, default = TRUE. |
data.type |
Choose from "main" and "imputed", default = "main". |
cluster.by |
Choose from "clusters" or "none", default = "clusters". |
conds.to.plot |
Choose the conditions you want to see in the plot, default = NULL (all conditions). |
min.scale |
Set a minimum color scale, default = -2.5. |
max.scale |
Set a maximum color scale, default = 2.5. |
interactive |
If TRUE an html interactive file will be made, default = TRUE. |
cex.col |
Chhose a size, default = 10. |
cex.row |
Choose a size, default = 10. |
no.key |
If you want a color legend key, default = FALSE. |
out.name |
Output name for html file if interactive = TRUE, default = "plot". |
heat.colors |
Colors for heatmap, default = c("blue" ,"white", "red"). |
An object of class iCellR
marker.genes <- findMarkers(demo.obj,fold.change = 2,padjval = 0.1,uniq = TRUE) MyGenes <- top.markers(marker.genes, topde = 10, min.base.mean = 0.8) heatmap.gg.plot(demo.obj, gene = MyGenes, out.name = "plot", cluster.by = "clusters", interactive = FALSE)