Creates ElbowPlot with ability to calculate and plot cutoffs for amount of variance conferred by the PCs. Cutoff 1 is PC where principal components only contribute less than 5% of standard deviation and the principal components cumulatively contribute 90% of the standard deviation. Cutoff 2 is point where the percent change in variation between the consecutive PCs is less than 0.1%.
ElbowPlot_scCustom(
seurat_object,
ndims = NULL,
reduction = "pca",
calc_cutoffs = TRUE,
plot_cutoffs = TRUE,
line_colors = c("dodgerblue", "firebrick"),
linewidth = 0.5
)Arguments
- seurat_object
name of Seurat object
- ndims
The number of dims to plot. Default is NULL and will plot all dims
- reduction
The reduction to use, default is "pca"
- calc_cutoffs
logical, whether or not to calculate the cutoffs, default is TRUE.
- plot_cutoffs
lgoical, whether to plot the cutoffs as vertical lines on plot, default is TRUE.
- line_colors
colors for the cutoff lines, default is c("dodgerblue", "firebrick").
- linewidth
widith of the cutoff lines, default is 0.5.
Value
ggplot2 object
References
Modified from following: https://hbctraining.github.io/scRNA-seq/lessons/elbow_plot_metric.html.
