The Full image
Ruqian Lyu
2024-08-22
Last updated: 2024-08-27
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ieny_2024_spatial-rna-graphs/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 7d0ce41 | rlyu | 2024-08-27 | full image figures |
| html | 65da68d | rlyu | 2024-08-27 | full image |
#.libPaths()
#setwd("/mnt/beegfs/mccarthy/backed_up/general/rlyu/Projects/ieny_2024_spatial-rna-graphs")
.libPaths( "/mnt/beegfs/mccarthy/backed_up/general/rlyu/Software/Rlibs/4.1.2")
suppressPackageStartupMessages({
library(readr)
library(ggplot2)
library(plotly)
library(dplyr)
})
#getwd()All testing results
all_res <- list.files("output/stable_train_gpu",
pattern = "ari_r.*.csv",
recursive = TRUE,full.names = T)
#length(all_res)
all_res <- sapply(all_res, function(x){ length(strsplit(x,"/")[[1]])})
all_res <- all_res[all_res ==7 ]
#length(all_res)
all_res <- names(all_res)
acc_results <- lapply(all_res,
function(file_name){
nedges = strsplit(file_name,"/")[[1]][3]
batch_size = strsplit(file_name,"/")[[1]][4]
h_size = strsplit(file_name,"/")[[1]][5]
radius = strsplit(file_name,"/")[[1]][7]
rep = strsplit(file_name,"/")[[1]][6]
acc_res = read.csv(file_name,header = 1,col.names = c("id","ari"))
acc_res$nedges = nedges
acc_res$rep = rep
acc_res$h_size = h_size
acc_res$batch_size = batch_size
acc_res$radius <- radius
acc_res[1:3,"id"] <- paste0("all_",acc_res[1:3,"id"])
acc_res[4:6,"id"] <- paste0("cell_",acc_res[4:6,"id"])
acc_res$type = c("all","all","all","cell","cell","cell")
acc_res
})Full image
p1 <- acc_results_df %>%
group_by(type,radius,nedges,rep,h_size,batch_size) %>%
arrange(-ari) %>%
slice(1) %>%
mutate(batch_size = factor(batch_size,
levels = c("batchsize100", "batchsize500",
"batchsize1024","batchsize2048" ))) %>%
mutate(h_size = factor(h_size,
levels = c( "hsize30","hsize50",
"hsize100","hsize150" ))) %>%
ggplot()+
geom_boxplot(mapping = aes(x = batch_size,
y = ari,fill=type),
outlier.shape = 12)+
geom_jitter(mapping = aes(x = batch_size,
y = ari),height = 0,
size=0.1)+
geom_hline(mapping=aes(yintercept=0.9),
linetype="dashed")+
facet_grid(cols = vars(nedges),rows = vars(radius,h_size),
scales = "free_x",
space="free_x")+
theme_bw(base_size = 10)+
theme(axis.text.x = element_text(angle = 90),
axis.title.x = element_blank())
p1
| Version | Author | Date |
|---|---|---|
| 97551da | rlyu | 2024-08-27 |
p_r1 <- acc_results_df %>%
group_by(type,radius,nedges,rep,h_size,batch_size) %>%
arrange(-ari) %>%
slice(1) %>%
filter(radius=="r1") %>%
mutate(batch_size = factor(batch_size,
levels = c("batchsize100", "batchsize500",
"batchsize1024","batchsize2048" ))) %>%
mutate(h_size = factor(h_size,
levels = c( "hsize30","hsize50",
"hsize100","hsize150" ))) %>%
ggplot()+
geom_boxplot(mapping = aes(x = batch_size,
y = ari,fill=type),
outlier.shape = 12)+
geom_jitter(mapping = aes(x = batch_size,
y = ari),height = 0,
size=0.1)+
geom_hline(mapping=aes(yintercept=0.9),
linetype="dashed")+
facet_grid(cols = vars(nedges),rows = vars(radius,h_size),
scales = "free_x",
space="free_x")+
theme_bw(base_size = 10)+
theme(axis.text.x = element_text(angle = 90),
axis.title.x = element_blank())
p_r3 <- acc_results_df %>%
group_by(type,radius,nedges,rep,h_size,batch_size) %>%
arrange(-ari) %>%
slice(1) %>%
filter(radius=="r3") %>%
mutate(batch_size = factor(batch_size,
levels = c("batchsize100", "batchsize500",
"batchsize1024","batchsize2048" ))) %>%
mutate(h_size = factor(h_size,
levels = c( "hsize30","hsize50",
"hsize100","hsize150" ))) %>%
ggplot()+
geom_boxplot(mapping = aes(x = batch_size,
y = ari,fill=type),
outlier.shape = 12)+
geom_jitter(mapping = aes(x = batch_size,
y = ari),height = 0,
size=0.1)+
geom_hline(mapping=aes(yintercept=0.9),
linetype="dashed")+
facet_grid(cols = vars(nedges),rows = vars(radius,h_size),
scales = "free_x",
space="free_x")+
theme_bw(base_size = 10)+
theme(axis.text.x = element_text(angle = 90),
axis.title.x = element_blank())
p_r6 <- acc_results_df %>%
group_by(type,radius,nedges,rep,h_size,batch_size) %>%
arrange(-ari) %>%
slice(1) %>%
filter(radius=="r6") %>%
mutate(batch_size = factor(batch_size,
levels = c("batchsize100", "batchsize500",
"batchsize1024","batchsize2048" ))) %>%
mutate(h_size = factor(h_size,
levels = c( "hsize30","hsize50",
"hsize100","hsize150" ))) %>%
ggplot()+
geom_boxplot(mapping = aes(x = batch_size,
y = ari,fill=type),
outlier.shape = 12)+
geom_jitter(mapping = aes(x = batch_size,
y = ari),height = 0,
size=0.1)+
geom_hline(mapping=aes(yintercept=0.9),
linetype="dashed")+
facet_grid(cols = vars(nedges),rows = vars(radius,h_size),
scales = "free_x",
space="free_x")+
theme_bw(base_size = 10)+
theme(axis.text.x = element_text(angle = 90),
axis.title.x = element_blank())radius r1 image
| Version | Author | Date |
|---|---|---|
| 97551da | rlyu | 2024-08-27 |
| Version | Author | Date |
|---|---|---|
| 97551da | rlyu | 2024-08-27 |
| Version | Author | Date |
|---|---|---|
| 97551da | rlyu | 2024-08-27 |
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.1.2 (2021-11-01)
os Rocky Linux 8.10 (Green Obsidian)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_AU.UTF-8
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tz Australia/Melbourne
date 2024-08-27
pandoc 3.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
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[2] /opt/R/4.1.2/lib/R/library
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