Some changes while reviewing docs with Louise

LieberInstitute · Aug 6, 2024 · 2a2532c · 2a2532c
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diff --git a/README.Rmd b/README.Rmd
@@ -48,7 +48,7 @@ BiocManager::install("LieberInstitute/DeconvoBuddies")
 ```
 ## Example
 
-```{r 'load_packages', echo = FALSE}
+```{r 'load_packages', warning = FALSE}
 suppressMessages({
     library("DeconvoBuddies")
     library("dplyr")
@@ -59,7 +59,7 @@ suppressMessages({
 
 
 ## Access Data
-Use `fetch_deconvo_data` Download RNA seqencing data from the Human DLPFC.  
+Use `fetch_deconvo_data` Download RNA sequencing data from the Human DLPFC.  
 
 * `rse_gene`: 110 samples of bulk RNA-seq. 
 
@@ -81,20 +81,30 @@ marker_stats <- get_mean_ratio(sce_DLPFC_example, cellType_col = "cellType_broad
 ```
 
 ### Extablish Color Scheme
+
 ```{r establish_colors}
 cell_types <- levels(sce_DLPFC_example$cellType_broad_hc)
-cell_colors <- create_cell_colors(cell_types = cell_types, pallet = "classic", split = "\\.", preview = TRUE)
+cell_colors <- create_cell_colors(
+    cell_types = cell_types,
+    pallet = "classic",
+    split = "\\.",
+    preview = TRUE
+)
 ```
 
 ### Plot Expression of Specified Genes
+
 Quickly create violin plot of gene expression. 
+
 ```{r plot_gene_expression}
 plot_gene_express(sce = sce_DLPFC_example, category = "cellType_broad_hc", genes = c("GAD2", "CD22"))
 plot_gene_express(sce = sce_DLPFC_example, category = "cellType_hc", genes = c("GAD2", "CD22"))
 ```
 
 ### Plot Expression of Marker Genes
+
 Plot the expression of top marker genes from the statistics calculated in `get_mean_ratio`.
+
 ```{r plot_marker_expression}
 plot_marker_express(sce_DLPFC_example,
     marker_stats,
@@ -106,6 +116,7 @@ plot_marker_express(sce_DLPFC_example,
 ```
 
 ### Create Composition Bar Plot
+
 ```{r composition_bar_plot}
 # extract phenotype data
 pd <- SummarizedExperiment::colData(rse_bulk_test) |>

diff --git a/README.md b/README.md
@@ -49,12 +49,18 @@ BiocManager::install("LieberInstitute/DeconvoBuddies")
 
 ## Example
 
-    #> Warning: package 'S4Vectors' was built under R version 4.4.1
-    #> Warning: package 'IRanges' was built under R version 4.4.1
+``` r
+suppressMessages({
+    library("DeconvoBuddies")
+    library("dplyr")
+    library("ggplot2")
+    library("SingleCellExperiment")
+})
+```
 
 ## Access Data
 
-Use `fetch_deconvo_data` Download RNA seqencing data from the Human
+Use `fetch_deconvo_data` Download RNA sequencing data from the Human
 DLPFC.
 
 - `rse_gene`: 110 samples of bulk RNA-seq.
@@ -65,7 +71,7 @@ DLPFC.
 
 ``` r
 if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
-#> 2024-08-02 10:50:28.235565 loading file /Users/louise.huuki/Library/Caches/org.R-project.R/R/BiocFileCache/58f79a421ca_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
+#> 2024-08-06 15:34:35.658167 loading file /Users/leocollado/Library/Caches/org.R-project.R/R/BiocFileCache/ae44256c3eb9_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1
 ```
 
 ## Marker Finding
@@ -82,7 +88,12 @@ marker_stats <- get_mean_ratio(sce_DLPFC_example, cellType_col = "cellType_broad
 
 ``` r
 cell_types <- levels(sce_DLPFC_example$cellType_broad_hc)
-cell_colors <- create_cell_colors(cell_types = cell_types, pallet = "classic", split = "\\.", preview = TRUE)
+cell_colors <- create_cell_colors(
+    cell_types = cell_types,
+    pallet = "classic",
+    split = "\\.",
+    preview = TRUE
+)
 ```
 
 <img src="man/figures/README-establish_colors-1.png" width="100%" />

diff --git a/vignettes/DeconvoBuddies.Rmd b/vignettes/DeconvoBuddies.Rmd
@@ -88,6 +88,8 @@ citation("DeconvoBuddies")
 
 # Quick start to using `DeconvoBuddies`
 
+Let's load some packages we'll use in this vignette.
+
 ```{r "load packages", message=FALSE}
 suppressMessages({
     library("DeconvoBuddies")
@@ -160,7 +162,12 @@ colors and makes your pallet flexible when considering different 'resolutions' o
 cell types. 
 ```{r create_cell_colors demo 2`}
 my_cell_types <- levels(sce_DLPFC_example$cellType_broad_hc)
-my_cell_colors <- create_cell_colors(cell_types = my_cell_types, pallet = "classic", preview = TRUE, split = "\\.")
+my_cell_colors <- create_cell_colors(
+    cell_types = my_cell_types,
+    pallet = "classic",
+    preview = TRUE,
+    split = "\\."
+)
 ```
 
 ### Plot Expression of Top Markers

diff --git a/vignettes/Deconvolution_Benchmark_DLPFC.Rmd b/vignettes/Deconvolution_Benchmark_DLPFC.Rmd
@@ -127,9 +127,6 @@ BiocManager::valid()
 ## Load Other Packages
 
 ```{r "load_packages", message=FALSE, warning=FALSE}
-## install Bisque from cran
-# install.packages("BisqueRNA")
-
 library("spatialLIBD")
 library("DeconvoBuddies")
 library("SummarizedExperiment")