plot_genes_positive_cells {monocle} | R Documentation |
@description Accetps a CellDataSet and a parameter,"grouping", used for dividing cells into groups. Returns one or more bar graphs (one graph for each gene in the CellDataSet). Each graph shows the percentage of cells that express a gene in the in the CellDataSet for each sub-group of cells created by "grouping".
Let's say the CellDataSet passed in included genes A, B, and C and the "grouping parameter divided all of the cells into three groups called X, Y, and Z. Then three graphs would be produced called A, B, and C. In the A graph there would be three bars one for X, one for Y, and one for Z. So X bar in the A graph would show the percentage of cells in the X group that express gene A.
plot_genes_positive_cells( cds_subset, grouping = "State", min_expr = 0.1, nrow = NULL, ncol = 1, panel_order = NULL, plot_as_fraction = TRUE, label_by_short_name = TRUE, relative_expr = TRUE, plot_limits = c(0, 100) )
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. |
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) |
plot_as_fraction |
whether to show the percent instead of the number of cells expressing each gene |
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 |
plot_limits |
A pair of number specifying the limits of the y axis. If NULL, scale to the range of the data. |
a ggplot2 plot object
## Not run: library(HSMMSingleCell) HSMM <- load_HSMM() MYOG_ID1 <- HSMM[row.names(subset(fData(HSMM), gene_short_name %in% c("MYOG", "ID1"))),] plot_genes_positive_cells(MYOG_ID1, grouping="Media", ncol=2) ## End(Not run)