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custom filenames for DT csv exports #115

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merged 6 commits into from
Jul 25, 2024
Merged

custom filenames for DT csv exports #115

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23a1ee1
rm general stats page
pdimens Jul 23, 2024
d4d72f9
add unique filenames for CSV exports
pdimens Jul 24, 2024
45b9590
add sample names
pdimens Jul 24, 2024
dbab9c9
fixes
pdimens Jul 24, 2024
93222ab
sentence case
pdimens Jul 24, 2024
940c12c
snake_case
pdimens Jul 24, 2024
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2 changes: 1 addition & 1 deletion .deprecated/align-minimap.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ rule genome_setup:
container:
None
message:
"copying {input} to Genome/"
"Copying {input} to Genome/"
shell:
"""
if (file {input} | grep -q compressed ) ;then
Expand Down
0 src/harpy/snakefiles/phase.bak.smk → .deprecated/phase.bak.smk
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6 changes: 5 additions & 1 deletion src/harpy/reports/align_bxstats.Rmd
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Expand Up @@ -128,7 +128,11 @@ DT::datatable(
aggregate_df,
rownames = F,
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
scrollX = TRUE,
buttons = list(list(extend = "csv",filename = "per_sample_barcode_alignment"))
),
caption = 'Per-Sample Alignment Information Pertaining to Barcodes',
fillContainer = T,
colnames = c("sample", "alignments", "unique molecules", "singletons", "multiplex", "unique barcodes", "molecule:bx ratio", "valid bx alignments", "invalid bx alignments", "% valid bx", "avg reads/molecule", "SEM reads/molecule", "avg molecule coverage %","SEM molecule coverage %", "N50", "N75","N90")
Expand Down
27 changes: 23 additions & 4 deletions src/harpy/reports/align_stats.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,14 @@ valueBox(scales::comma(totuniqBX), caption = "Total unique molecules", color = "
valids %>%
group_by(contig) %>%
summarize(n50 = NX(length_inferred, 50), n75 = NX(length_inferred, 75), n90 = NX(length_inferred, 90)) %>%
DT::datatable(rownames = F, options = list(dom = 'Brtip', buttons = c('csv')), fillContainer = T)
DT::datatable(
rownames = F,
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = paste0(samplename ,"_molecule_NX")))
),
fillContainer = T
)
```

## Reads per molecule dec
Expand Down Expand Up @@ -446,7 +453,11 @@ DT::datatable(
contig_avg,
rownames = F,
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
scrollX = TRUE,
buttons = list(list(extend = "csv",filename = paste0(samplename ,"_align_depth_avg")))
),
colnames = c('Contig', 'Average Depth', 'Standard Deviation'),
autoHideNavigation = T,
fillContainer = T,
Expand All @@ -460,7 +471,11 @@ DT::datatable(
contig_avg_filt,
rownames = F,
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
scrollX = TRUE,
buttons = list(list(extend = "csv",filename = paste0(samplename ,"_align_depth_filt_avg")))
),
colnames = c('Contig', 'Average Depth', 'Standard Deviation'),
autoHideNavigation = T,
fillContainer = T,
Expand All @@ -474,7 +489,11 @@ DT::datatable(
outliers,
rownames = F,
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
scrollX = TRUE,
buttons = list(list(extend = "csv",filename = paste0(samplename ,"_align_depth_outlier_avg")))
),
colnames = c('Contig', 'Position', 'Depth'),
autoHideNavigation = T,
fillContainer = T
Expand Down
15 changes: 13 additions & 2 deletions src/harpy/reports/bcftools_stats.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -255,7 +255,7 @@ if(sum(.dpL) == 0){
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv')),
options = list(dom = 'Brtip', buttons = list(list(extend = "csv",filename = "align_depth_bins"))),
colnames = c("Depth Bin", "Genotypes", "% Genotypes", "Sites", "% Sites")
)
}
Expand Down Expand Up @@ -317,7 +317,18 @@ figheight <- 1 + (0.2 * nrow(psc))
## Individual Statistics {.tabset data-height=plotheight}
### Individual Data
```{r Individual table, echo=FALSE, message=FALSE, warning=FALSE}
DT::datatable(psc, rownames = F, fillContainer = T, filter = "top", extensions = 'Buttons', options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE, paging = F))
DT::datatable(
psc, rownames = F,
fillContainer = T,
filter = "top",
extensions = 'Buttons',
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "snp_indiv_stats")),
scrollX = TRUE,
paging = F
)
)
```

### Individual Statistics
Expand Down
14 changes: 11 additions & 3 deletions src/harpy/reports/hapcut.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -179,10 +179,14 @@ DT::datatable(
percontig,
rownames = F,
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "phasing_per_contig")),
scrollX = TRUE
),
colnames = c("Contig", "Total Haplotypes", "Mean SNPs", "Median SNPs", "Mean Haplotype Length", "Median Haplotype Length", "Largest Haplotype"),
fillContainer = T
)
)
```

### per contig plot {.no-title}
Expand Down Expand Up @@ -247,7 +251,11 @@ DT::datatable(
persample,
rownames = F,
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "phasing_per_sample")),
scrollX = TRUE
),
colnames = c("Sample", "Haplotypes", "Mean SNPs", "Median SNPs", "Mean Haplotype Length", "Median Haplotype Length", "Largest Haplotype"),
fillContainer = T
)
Expand Down
13 changes: 10 additions & 3 deletions src/harpy/reports/leviathan.Rmd
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Expand Up @@ -27,7 +27,6 @@ using<-function(...) {
using("flexdashboard","dplyr","ggplot2","DT","BioCircos")
```

# General Stats
## Intro
### introtext {.no-title}
```{r}
Expand Down Expand Up @@ -127,7 +126,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = paste0(samplename , "_sv_leviathan`"))),
scrollX = TRUE
),
autoHideNavigation = T,
fillContainer = T
)
Expand All @@ -148,7 +151,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = paste0(samplename ,"_sv_leviathan_per_contig"))),
scrollX = TRUE
),
autoHideNavigation = T,
fillContainer = T
)
Expand Down
18 changes: 15 additions & 3 deletions src/harpy/reports/leviathan_pop.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "leviathan_sv")),
scrollX = TRUE
),
fillContainer = T
)
```
Expand All @@ -158,7 +162,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "leviathan_sv_count_pop")),
scrollX = TRUE
),
fillContainer = T
)
```
Expand All @@ -177,7 +185,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "leviathan_sv_bp_pop")),
scrollX = TRUE
),
fillContainer = T
)
```
Expand Down
28 changes: 20 additions & 8 deletions src/harpy/reports/naibr.Rmd
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Expand Up @@ -23,7 +23,6 @@ fai <- snakemake@input[["fai"]]
samplename <- gsub(".bedpe", "", basename(infile))
```

# General Stats
## file top
### file header {.no-title}
<h1> NAIBR Variant Calling: `r samplename` </h1>
Expand Down Expand Up @@ -145,8 +144,11 @@ DT::datatable(
grpstats %>% pivot_wider(id_cols = 1, names_from = SV, values_from = count),
rownames = F,
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
#colnames = c('Contig', 'Variant Type', 'Count', 'Total Base Pairs'),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = paste0(samplename , "_sv_naibr_count"))),
scrollX = TRUE
),
autoHideNavigation = T,
fillContainer = T
)
Expand All @@ -157,9 +159,11 @@ DT::datatable(
grpstats %>% pivot_wider(id_cols = 1, names_from = SV, values_from = total_bp),
rownames = F,
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
#colnames = c('deletion', 'duplication', 'inversion'),
autoHideNavigation = T,
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = paste0(samplename , "_sv_naibr_count_bp"))),
scrollX = TRUE
), autoHideNavigation = T,
fillContainer = T,
)
```
Expand Down Expand Up @@ -210,7 +214,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = paste0(samplename ,"_sv_naibr"))),
scrollX = TRUE
),
autoHideNavigation = T,
fillContainer = T
)
Expand All @@ -222,7 +230,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = paste0(samplename ,"_sv_naibr_chimeric"))),
scrollX = TRUE
),
autoHideNavigation = T,
fillContainer = T
)
Expand Down
24 changes: 20 additions & 4 deletions src/harpy/reports/naibr_pop.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -172,7 +172,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "naibr_sv_count_pop")),
scrollX = TRUE
),
fillContainer = T
)
```
Expand All @@ -189,7 +193,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "naibr_sv_count_bp")),
scrollX = TRUE
),
fillContainer = T
)
```
Expand Down Expand Up @@ -239,7 +247,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = 'csv', scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "naibr_sv")),
scrollX = TRUE
),
fillContainer = T
)
```
Expand All @@ -250,7 +262,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE)
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "naibr_sv_chimeric")),
scrollX = TRUE
)
)
```

Expand Down
6 changes: 5 additions & 1 deletion src/harpy/reports/preflight_bam.Rmd
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Expand Up @@ -133,7 +133,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = T),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "bam_checks")),
scrollX = T
),
fillContainer = T
)
```
Expand Down
6 changes: 5 additions & 1 deletion src/harpy/reports/preflight_fastq.Rmd
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Expand Up @@ -129,7 +129,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = T),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "fastq_checks")),
scrollX = T
),
fillContainer = T
)
```
Expand Down
6 changes: 5 additions & 1 deletion src/harpy/reports/stitch_collate.Rmd
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Expand Up @@ -145,7 +145,11 @@ DT::datatable(
rownames = F,
filter = "top",
extensions = 'Buttons',
options = list(dom = 'Brtip', buttons = c('csv'), scrollX = TRUE),
options = list(
dom = 'Brtip',
buttons = list(list(extend = "csv",filename = "impute_per_sample")),
scrollX = TRUE
),
autoHideNavigation = T,
fillContainer = T
)
Expand Down
2 changes: 1 addition & 1 deletion src/harpy/snakefiles/align_bwa.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ rule genome_setup:
container:
None
message:
"copying {input} to Genome/"
"Copying {input} to Genome/"
shell:
"""
if (file {input} | grep -q compressed ) ;then
Expand Down
2 changes: 1 addition & 1 deletion src/harpy/snakefiles/align_ema.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ rule genome_setup:
container:
None
message:
"copying {input} to Genome/"
"Copying {input} to Genome/"
shell:
"""
if (file {input} | grep -q compressed ) ;then
Expand Down
2 changes: 1 addition & 1 deletion src/harpy/snakefiles/align_strobealign.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ rule genome_setup:
container:
None
message:
"copying {input} to Genome/"
"Copying {input} to Genome/"
shell:
"""
if (file {input} | grep -q compressed ) ;then
Expand Down
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