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Remove R script/notebook package installs from gene-set-enrichment and ATRT (Part 3 of N) #703

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merged 5 commits into from
May 23, 2020
Merged

Remove R script/notebook package installs from gene-set-enrichment and ATRT (Part 3 of N) #703

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5fb6c87
Remove package installs from gsea
cansavvy May 21, 2020
b2381f2
Get rid of installations in ATRT and rerun
cansavvy May 21, 2020
0f1211e
Merge branch 'master' into cansavvy-remove-r-package-installs-3
cansavvy May 22, 2020
06739ed
Merge branch 'master' into cansavvy-remove-r-package-installs-3
jaclyn-taroni May 23, 2020
363512d
Merge branch 'master' into cansavvy-remove-r-package-installs-3
jaclyn-taroni May 23, 2020
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11 changes: 1 addition & 10 deletions analyses/gene-set-enrichment-analysis/01-conduct-gsea-analysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,16 +34,6 @@ library(optparse)
# Magrittr pipe
`%>%` <- dplyr::`%>%`

if (!("msigdbr" %in% installed.packages())) {
install.packages("msigdbr")
}
if (!("BiocManager" %in% installed.packages())) {
install.packages("BiocManager")
}
library(BiocManager, quietly = TRUE)
if (!("GSVA" %in% installed.packages())) {
BiocManager::install("GSVA")
}
library(msigdbr) ## Contains the hallmark data sets
library(GSVA) ## Performs GSEA analysis

Expand All @@ -69,6 +59,7 @@ option_list <- list(
## Read in arguments
opt_parser <- optparse::OptionParser(option_list = option_list)
opt <- optparse::parse_args(opt_parser)

if (is.na(opt$input_file)) stop("\n\nERROR: You must provide an input file with expression data with the flag --input, assumed to be in the `data/` directory of the OpenPBTA repository..")
if (is.na(opt$output_file)) stop("\n\nERROR: You must provide an output file for saving GSVA scores with the flag --output, assumed to be placed in the `results/` directory of this analysis.")

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8 changes: 0 additions & 8 deletions analyses/molecular-subtyping-ATRT/01-ATRT-molecular-subtyping-data-prep.Rmd
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Expand Up @@ -22,14 +22,6 @@ of the repository as follows:
```{r}
# Get `magrittr` pipe
`%>%` <- dplyr::`%>%`

# Install `DT` and `htmlwidgets` packages for displaying tables
if (!("DT" %in% installed.packages())) {
install.packages("DT")
}
if (!("htmlwidgets" %in% installed.packages())) {
install.packages("htmlwidgets")
}
```

## Directories and Files
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18 changes: 5 additions & 13 deletions analyses/molecular-subtyping-ATRT/01-ATRT-molecular-subtyping-data-prep.nb.html
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18 changes: 2 additions & 16 deletions analyses/molecular-subtyping-ATRT/02-ATRT-molecular-subtyping-plotting.R
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Expand Up @@ -12,20 +12,6 @@

#### Set Up --------------------------------------------------------------------

# Install and load in ComplexHeatMap
if (!("ComplexHeatmap" %in% installed.packages())) {
install.packages("ComplexHeatmap")
}
library(ComplexHeatmap)
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I accidentally deleted this so I ended up adding in the necessary ComplexHeatmap:: bits.


if (!("matrixStats" %in% installed.packages())) {
install.packages("matrixStats")
}

if (!("ggfortify" %in% installed.packages())) {
install.packages("ggfortify")
}

library(ggfortify)
library(dplyr)

Expand Down Expand Up @@ -102,7 +88,7 @@ annotation_df <- final_df %>%
tibble::column_to_rownames("sample_id")

# Make into an annotation object
column_annotation <- HeatmapAnnotation(df = annotation_df)
column_annotation <- ComplexHeatmap::HeatmapAnnotation(df = annotation_df)

# Plot and save the Heatmap
png(
Expand All @@ -111,7 +97,7 @@ png(
height = 604,
units = "px"
)
Heatmap(
ComplexHeatmap::Heatmap(
high_var_exp,
heatmap_legend_param = list(title = "zscore"),
top_annotation = column_annotation,
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Binary file modified analyses/molecular-subtyping-ATRT/plots/atrt_heatmap.png
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