plot_genes_violin {monocle} | R Documentation |
Accepts a subset of a CellDataSet and an attribute to group cells by, and produces one or more ggplot2 objects that plots the level of expression for each group of cells.
plot_genes_violin(cds_subset, grouping = "State", min_expr = NULL, cell_size = 0.75, nrow = NULL, ncol = 1, panel_order = NULL, color_by = NULL, plot_trend = FALSE, label_by_short_name = TRUE, relative_expr = TRUE, log_scale = TRUE)
cds_subset |
CellDataSet for the experiment |
grouping |
the cell attribute (e.g. the column of pData(cds)) to group cells by on the horizontal axis |
min_expr |
the minimum (untransformed) expression level to use in plotted the genes. |
cell_size |
the size (in points) of each cell used in the plot |
nrow |
the number of rows used when laying out the panels for each gene's expression |
ncol |
the number of columns used when laying out the panels for each gene's expression |
panel_order |
the order in which genes should be layed out (left-to-right, top-to-bottom) |
color_by |
the cell attribute (e.g. the column of pData(cds)) to be used to color each cell |
plot_trend |
whether to plot a trendline tracking the average expression across the horizontal axis. |
label_by_short_name |
label figure panels by gene_short_name (TRUE) or feature id (FALSE) |
relative_expr |
Whether to transform expression into relative values |
log_scale |
a boolean that determines whether or not to scale data logarithmically |
a ggplot2 plot object
## Not run: library(HSMMSingleCell) HSMM <- load_HSMM() my_genes <- HSMM[row.names(subset(fData(HSMM), gene_short_name %in% c("ACTA1", "ID1", "CCNB2"))),] plot_genes_violin(my_genes, grouping="Hours", ncol=2, min_expr=0.1) ## End(Not run)