libraries
suppressPackageStartupMessages({
library(scater)
library(ggtern)
library(gridExtra)
library(scran)
library(cowplot)
library(dplyr)
library(magrittr)
library(purrr)
library(jcolors)
library(hrbrthemes)
library(tidyr)
library(here)
})
Data
#data_path <- c("/run/user/1000/gvfs/sftp:host=imlsportmacquarie.uzh.ch/home/aluetg/batch_characterization/batch_snakemake/out/sim_variance_part_ct/")
data_path <- params$data_path
datasets <- list.files(path = data_path, pattern = "sce.rds")
cols_data <-c(c(jcolors('pal6'),jcolors('pal8'))[c(1,8,14,2:4,6,12:13,15:20)],jcolors('pal4'))
names(cols_data) <- c()
out_path <- params$out_path
Ternary plots
#prepare data frame
prep_data <- function(dat){
data_nam <- gsub("vp_ct_", "", dat) %>% gsub("_sce.rds", "",.)
sce <- readRDS(paste0(data_path, dat))
type <- grep("_ct$", names(rowData(sce)), value = TRUE)
tab <- as.data.frame(rowData(sce)[,type])
tab$dataset <- rep(data_nam, nrow(tab))
rm(sce)
gc()
tab
}
type_data <- datasets %>% map(prep_data) %>% bind_rows()
type_data$dataset <- as.factor(type_data$dataset)
type_data <- type_data %>% dplyr::filter(vp_residuals_ct < 0.95)
Plot
t1 <- ggtern(data=type_data, aes(vp_celltype_ct, vp_batch_ct, vp_cellt_by_batch_ct)) +
guides(color = guide_legend(override.aes = list(size = 3, alpha = 1))) +
geom_point(aes(colour = dataset),size= 1.6, alpha = 0.9) +
scale_colour_manual(values = cols_data) +
#stat_density_tern(aes(fill=..level.., alpha=..level..),geom='polygon',bdl = 0.01,bdl.val = 1, base = "identity", n = 20) +
geom_density_tern(
bins=10,
bdl = 0.02,
color='black',
base = "identity", n = 20,
bdl.val = 0.1) +
Llab("cell\n \t type") +
Tlab("batch") +
Rlab("int.") +
ggtitle("Percent variance explained by ...:") +
theme_ipsum(axis = TRUE,
base_family = 'Helvetica',
base_size = 19,
axis_title_size = 20,
strip_text_face = "bold",
grid_col = "#cccccc",
plot_margin = margin(0, 0, 0, 0)) +
facet_wrap(~dataset, ncol = 2) +
theme(plot.title = element_text(size=24, hjust = 0.3),
plot.subtitle = element_text(size=20),
panel.grid.major = element_blank(),
axis.text.x = element_blank(),
axis.text.y = element_blank(),
panel.spacing = unit(0.2, "lines"),
legend.position = "none",
strip.text = element_text(face="bold", size=22)
)
t1
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
saveRDS(t1, paste0(out_path, "ternary_ct_sim.rds"))
ggtern::ggsave(filename = paste0(out_path, "ternary_ct_sim.pdf"), plot = t1, dpi = 600)
## Saving 9 x 18 in image
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning: Computation failed in `stat_density_tern()`:
## unused argument (z.range = z.range)
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font width unknown for character 0x9
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font width unknown for character 0x9
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font width unknown for character 0x9
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
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## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font width unknown for character 0x9
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font width unknown for character 0x9
## Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
## font width unknown for character 0x9