plot_pair_scatter: Plot Pairwise Gene Scatter Plot

In robustSingleCell: Robust Clustering of Single Cell RNA-Seq Data

Description

Visualize normalized expression contours of a selected gene pair across selected cluster groups.

Usage

plot_pair_scatter(environment, gene1, gene2, cluster_group1,
  cluster_group2, group1_label, group2_label, width = 10, height = 10)

Arguments

environment	environment object
gene1	selected gene number 1
gene2	selected gene number 2
cluster_group1	cluster group 1 to be visualized (one or more clusters)
cluster_group2	cluster group 2 to be visualized (one or more clusters)
group1_label	label for group 1 legend and file name
group2_label	label for group 2 legend and file name
width	pdf file canvas width
height	pdf file canvas height

Examples

LCMV1 <- setup_LCMV_example()
LCMV1 <- get.variable.genes(LCMV1, min.mean = 0.1, min.frac.cells = 0,
min.dispersion.scaled = 0.1)
LCMV1 <- PCA(LCMV1)
LCMV1 <- cluster.analysis(LCMV1)
cluster_names <- get.cluster.names(LCMV1, types, min.fold = 1.0, max.Qval = 0.01)
LCMV1 <- set.cluster.names(LCMV1, names = cluster_names)
plot_pair_scatter(LCMV1,
gene1 = 'Cd4',
gene2 = 'Cd8',
cluster_group1 = cluster_names[1:2],
cluster_group2 = cluster_names[3:4],
group1_label = 'CD4 T Cells',
group2_label = 'CD8 T Cells')

robustSingleCell documentation built on May 2, 2019, 2:11 p.m.