plot_forceDirectedGraph_label_by_multiple_gene_sets_with_limited_sampleID | R Documentation |
Plot force-directed graph with the expression of multiple gene sets on selected sample IDs
plot_forceDirectedGraph_label_by_multiple_gene_sets_with_limited_sampleID(
object,
gmt.file = c(),
selected.sampleID = c(),
title = "",
show_gene_sets = c(),
custom_color = c(),
IsDownsample = F,
downsample.size = 0,
isNormalizedByHouseKeeping = T,
vertex.size = 1.5,
edge.size = 0.2,
edge.color = "gray",
title.color = "red",
title.font.size = 16,
showLegend = T,
background.color = "white"
)
object |
The SingCellaR object. |
gmt.file |
The GMT file. |
selected.sampleID |
Selected sample IDs |
title |
The title of the plot. |
show_gene_sets |
The name of gene sets to be shown. |
custom_color |
The vector of cutom color to specify gene sets. |
IsDownsample |
is logical. If TRUE, the cells will be downsampled. |
downsample.size |
The number of cells for the downsample. Default 0 |
isNormalizedByHouseKeeping |
is logical. If TRUE, the gene expression will be normalized by the expression of house keeping genes. |
vertex.size |
The point size. Default 1.5 |
edge.size |
The edge size. Default 0.2 |
edge.color |
The edge color. Default gray |
title.color |
The color of the title. Default red |
title.font.size |
The title font size. Default 16 |
showLegend |
is logical. If TRUE, the figure legend will be displayed. |
background.color |
The background color. Default white |
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