View source: R/composition_plot.R
composition_plot | R Documentation |
This function returns a list where the 1st element is plot composition representing the absolute number and proportion of a variable grouped by a feature of interest and the 2nd are the individual plots..
composition_plot( metadata, x, grouping_vr, gradient_col = c("#7ab2ff", "#ffc157", "#fa5e25"), col_df = NULL, x_order = NULL, grouping_order = NULL, title = "", label = FALSE )
metadata |
metadata from the Seurat object - se_obj\@meta.data |
x |
character string indicating the X axis - cell type annotation |
grouping_vr |
character string specifying the feature to group the data by - condition |
gradient_col |
vector of n colors indicating the color gradient to use in the proportion tile plot |
col_df |
data frame with variables name and color containing the name - color pair |
x_order |
character string vector containing the x names in the desired order |
grouping_order |
character string vector containing the grouping names in the desired order |
title |
character string indicating the plot title, by default and empty string "" |
label |
Logical vector indicating if we want to show proportion labels in the tile plot. By default FALSE. |
Composition plot
## Not run: library(Seurat) library(SeuratData) # SeuratData::InstallData(ds = "pbmcsca") se_obj <- SeuratData::LoadData(ds = "pbmcsca") col_df <- data.frame( "name" = unique(se_obj@meta.data$CellType), "color" = terrain.colors(10) ) grouping_order <- c("Cytotoxic T cell", "CD4+ T cell", "CD14+ monocyte", "B cell", "Megakaryocyte", "CD16+ monocyte", "Natural killer cell", "Dendritic cell", "Plasmacytoid dendritic cell", "Unassigned") SCrafty::composition_plot( metadata = se_obj@meta.data, x = "Method", grouping_vr = "CellType", gradient_col = rainbow(5), col_df = col_df, x_order = unique(se_obj@meta.data$Method), grouping_order = grouping_order, title = "Distribution of cells over methods", label = TRUE ) ## End(Not run)
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