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Author: cparsania

articles/VISTA-airway.html

@@ -903,6 +903,20 @@ get_expression_barplot(
 
 ![](VISTA-airway_files/figure-html/barplot-log-stats-1.png)
 
+#### Per-sample barplot for selected genes
+
+``` r
+get_expression_barplot(
+  vista,
+  genes = top_up$gene_id[1:2],
+  display_id = "SYMBOL",
+  by = "sample",
+  sample_order = "group"
+)
+```
+
+![](VISTA-airway_files/figure-html/barplot-per-sample-1.png)
+
 #### Compare up and down regulated genes
 
 ``` r
@@ -1105,6 +1119,20 @@ get_expression_lollipop(
 
 ![](VISTA-airway_files/figure-html/lollipop-plot-1.png)
 
+#### Per-sample lollipop plot
+
+``` r
+get_expression_lollipop(
+  vista,
+  genes = top_up$gene_id[1:2],
+  display_id = "SYMBOL",
+  by = "sample",
+  sample_order = "expression"
+)
+```
+
+![](VISTA-airway_files/figure-html/lollipop-per-sample-1.png)
+
 #### Joyplot by treatment group
 
 ``` r
@@ -1644,6 +1672,36 @@ head(fc_matrix, n = 10)
 #> ENSG00000001461                -0.04363732
 ```
 
+### Fold-change Barplot and Lollipop
+
+#### Per-gene fold-change barplot
+
+``` r
+get_foldchange_barplot(
+  vista,
+  genes = top_up$gene_id[1:3],
+  sample_comparisons = comp_names,
+  display_id = "SYMBOL",
+  facet_by = "gene"
+)
+```
+
+![](VISTA-airway_files/figure-html/fc-barplot-gene-1.png)
+
+#### Per-gene fold-change lollipop
+
+``` r
+get_foldchange_lollipop(
+  vista,
+  sample_comparison = comp_names[1],
+  genes = top_up$gene_id[1:3],
+  display_id = "SYMBOL",
+  facet_by = "gene"
+)
+```
+
+![](VISTA-airway_files/figure-html/fc-lollipop-gene-1.png)
+
 ### Fold-change Raincloud
 
 ``` r

articles/VISTA-airway.md

@@ -494,7 +494,7 @@ Visualize gene expression patterns across samples and groups.
 - [`get_expression_heatmap()`](get_expression_heatmap.md) : Expression
   heatmap
 - [`get_expression_barplot()`](get_expression_barplot.md) : Plot gene
-  expression means with optional statistics
+  expression as barplots
 - [`get_expression_boxplot()`](get_expression_boxplot.md) : Plot gene
   expression distributions as boxplots
 - [`get_expression_violinplot()`](get_expression_violinplot.md) : Violin
@@ -505,8 +505,8 @@ Visualize gene expression patterns across samples and groups.
   normalized expression between two samples or groups
 - [`get_expression_lineplot()`](get_expression_lineplot.md) : Gene
   expression line plot
-- [`get_expression_lollipop()`](get_expression_lollipop.md) : Plot mean
-  expression per group as a lollipop chart
+- [`get_expression_lollipop()`](get_expression_lollipop.md) : Plot
+  expression as a lollipop chart
 - [`get_expression_joyplot()`](get_expression_joyplot.md) : Plot
   expression distributions as ridgelines
 - [`get_expression_raincloud()`](get_expression_raincloud.md) :