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Fixed more typos #8

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Merged
sameet merged 3 commits into from
Sep 29, 2023
Merged

Fixed more typos #8

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7623c08
fixed the abstraction issue introduced in devel
sameetmehta Sep 29, 2023
0c50965
Fixed a typo.
sameetmehta Sep 29, 2023
487207a
Fixed a typo, and make sure the output directory is created.
sameetmehta Sep 29, 2023
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18 changes: 12 additions & 6 deletions R/qmd_template_parts.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@
#' @param title Title for the report
#' @param author Author for the report
#' @param email Email of the author for the report
#' @param ... Other parameters to set the yaml header
#'
#' @return opening_yaml string to be used to construct the report qmd
#' @export
Expand All @@ -15,7 +14,13 @@
template_yaml <- function(title = "RNA-Seq Report",
author = "Sameet",
email = "sameet.mehta@yale.edu",
...) {
count_fn = "gene_count_matrix.csv",
sample_fn = "sample-sheet.txt",
contrast_fn = "contrasts.txt",
metrics = NULL,
outputdir = "rnaseq_report_outputs",
thresh = 0.05
) {
opening_yaml <- stringr::str_glue("
---
title: \"{title}\"
Expand All @@ -41,7 +46,7 @@ params:
contrasts_fn: null
metrics: null
outputs: \"{outputdir}\"
use_threshold: 0.05
use_threshold: {thresh}
---
")
opening_yaml
Expand Down Expand Up @@ -74,6 +79,7 @@ We will import packages and functions.

library(quartoReport)
# use_thresh <- 0.05 # global threshold to use as alpha in the analysis
if(!dir.exists(params$outputs)) dir.create(params$outputs)
```

Please note that this package is currently under active development.
Expand Down Expand Up @@ -387,16 +393,16 @@ This is a deconstructed Venn Diagram that is much more interpretable.
Upset plot for the data in this analysis is given in @fig_upset

```{{r}}
#| label: fig_upset
#| label: fig-upset
#| fig-cap: UpSet plot with with significant genes seen across all the comparisons.

upset_df <- make_upset_df(dds = dds, meta_df = meta_df,
contrasts_df = contrasts_df, thresh = params$use_threshold)
upset_plot <- make_upset_plot(upset_df)
ofn_upset <- file.path(params$outputs, \"upset-plot.pdf\")
ggplot2::ggsave(filname = ofn_upset, device = \"pdf\", plot = upset_plot)
ggplot2::ggsave(filename = ofn_upset, device = \"pdf\", plot = upset_plot)
upset_plot
```
In @fig_upset the number in the bars denotes number of genes satisfying that condition.
In @fig-upset the number in the bars denotes number of genes satisfying that condition.
")
}