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Update output of kable tables from .png to .pdf #1

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Update output of kable tables from .png to .pdf #1

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17 changes: 11 additions & 6 deletions scripts/Hackflex_data_analysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ library(data.table)
library(gridExtra)
library(grid)
library(stringr)
library(kableExtra)
library(knitr)
library(kableExtra) # S: kableExtra is dependant on knitr, inverting the load order could break something



Expand Down Expand Up @@ -591,7 +591,10 @@ fwrite(x=ME_data, file=paste0(mydir,"Alfred_ME_data.csv"))


# plot
pdf(paste0(mydir,species,'_out.pdf'))

# S: TODO create dir before pdf() function
pdf(paste0(mydir,species,'_out.pdf')) # S: could give error: cannot create file '[filename]', reason 'No such file or directory'

# plot coverage
ggarrange(p1,p2,
labels = c("A","B"),
Expand Down Expand Up @@ -667,15 +670,17 @@ dev.off()

# stats libs before, after cleaning and after resizing :
x <- cbind(read_lengths[,1:4],n_reads[,2:4],n_bp[,2:4])
kbl(x, "html") %>%
kable(x, "html") %>%
kable_classic() %>%
add_header_above(c(" " = 1, "average read length" = 3, "# reads" = 3, "# bp" = 3)) %>%
as_image(width=7, file = paste0(mydir,species,"_stats.png"))
# as_image(width=7, file = paste0(mydir,species,"_stats.png")) # S: TODO cleanup later
save_kable(file = paste0(mydir,species,"_stats.pdf"))
class(sp)
# stats coverage :
kbl(ME_data, "html") %>%
kable(ME_data, "html") %>%
kable_classic() %>%
as_image(width=7, file = paste0(mydir,species,"_cov_stats.png"))
# as_image(width=7, file = paste0(mydir,species,"_cov_stats.png")) # S: TODO cleanup later
save_kable(file = paste0(mydir,species,"_cov_stats.pdf"))



Expand Down