plot_vln_Corgenes
plot_vln_Corgenes.RdMake grid of violin plots Thanks to the SCOPfunctions package https://github.com/CBMR-Single-Cell-Omics-Platform/SCOPfunctions/blob/main/R/plot.R
produce a n_celltype * n_genes grid of violin plots
Usage
plot_vln_Corgenes(
seurat_obj,
assay,
slot,
var_group,
vec_features,
vec_group_colors = NULL,
f_color = grDevices::colorRampPalette(RColorBrewer::brewer.pal(n = 11, name =
"RdYlBu")),
flip = T,
do_plot = FALSE,
pt.size = 0,
feature_fontface = "bold.italic",
fontsize_axistext_x = 12,
fontsize_axistext_y = 12,
aspect.ratio = NULL,
figurenames = NULL,
width = 7,
height = 7
)Arguments
- seurat_obj
Seurat object (Seurat ^3.0)
- assay
seurat_obj assay to use
- slot
seurat_obj slot to use
- var_group
the group variable, character
- vec_features
a vector of features to plot in the violin plot
- vec_group_colors
a vector of colors, named by corresponding group. Length must match number of groups. Character
- f_color
if vec_group_colors is not provided, the user may instead provide a function f_color() that takes as its only argument the number of colors to generate
- flip
if TRUE (default), groups are rows and features are columns, and vice-verso for FALSE
- do_plot
Whether to plot, logical
- pt.size
size of jitter in the violin plots. Set to 0 (default) to omit
- feature_fontface
"bold.italic"
- fontsize_axistext_x
12, font size for x axis
- fontsize_axistext_y
12, font size for y axis
- aspect.ratio
NULL
- figurenames
The filename and address of the output plot,
- width
figure width
- height
figure height
Examples
load(system.file("extdata", "Pagwas_data.RData", package = "scPagwas"))
suppressMessages(library("ggsci"))
suppressMessages(library("Seurat"))
top5genes <- rownames(Pagwas_data@misc$gene_heritability_correlation)[order(
Pagwas_data@misc$gene_heritability_correlation,
decreasing = TRUE
)[1:5]]
plot_vln_Corgenes(
seurat_obj = Pagwas_data,
assay = "RNA", slot = "data",
var_group = "anno",
vec_features = top5genes,
do_plot = TRUE
)
#> Using aspect ratio 3
