Description Usage Arguments Value Examples
pseudotimeplotByGenes
1 2 3 4 | pseudotimePlotByGenes(exprs, if_log2 = TRUE, cell_annotation, cell_order,
plot_genes = NULL, reverse_order = FALSE, min_expr = -3,
cell_size = 2, plot_cols = NULL,
trend_formula = "expression ~ sm.ns(Pseudotime, df=3)")
|
exprs |
a data frame or matrix of log transformed expression data, with row of cells and column of genes |
if_log2 |
whether exprs is log2 transformed |
cell_annotation |
a two column data frame of matrix annotating cells(cell ID or name) with cell types |
cell_order |
a vector stroing the order of cells with cell ID or name, same as appeared in row names of |
plot_genes |
a vector storing the genes selected for plot, same as appeared in the column names of |
reverse_order |
reverse the order of the pseudotime |
min_expr |
the threshold for cutting of the cell expressions in regression values, values lower than this will be forced to |
cell_size |
the size of cells in the plot |
plot_cols |
plot colours |
trend_formula |
the formula for regression analysis |
a object of ggplot
1 2 3 4 5 6 7 8 | ## Not run:
pseudotimePlotByGenes(exprs = "FULL.log2TPM.txt",
cell_annotation = "splAnnotation_outlierRemoved.txt",
cell_order = "uspin.PCA.0.03.seed1.txt",
plot_genes = "genes.txt",
reverse_order = TRUE, plot_cols = 3)
## End(Not run)
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