Standardize batch correction figure behavior across function calls

.codeocean/app-panel.json

@@ -17,6 +17,24 @@
 			"name": "Basic",
 			"icon": "📂"
 		},
+		{
+			"id": "VisGeneral",
+			"name": "Visualization: General",
+			"description": "General visualization and plotting options",
+			"icon": "\ud83d\udcca"
+		},
+		{
+			"id": "VisPCA",
+			"name": "Visualization: PCA",
+			"description": "PCA plot options",
+			"icon": "\ud83d\udcca"
+		},
+		{
+			"id": "VisHistogram",
+			"name": "Visualization: Histogram",
+			"description": "Histogram plot options",
+			"icon": "\ud83d\udcca"
+		},
 		{
 			"id": "XqgPq28Eo5VCFSZu",
 			"name": "Advanced",
@@ -25,6 +43,22 @@
 		}
 	],
 	"parameters": [
+		{
+			"id": "UA4GuIpVAxdcmHAG",
+			"category": "gn9FXwemlVazWQIo",
+			"name": "Count type",
+			"param_name": "count_type",
+			"description": "Type of counts to batch correct. Must be a count type in names(moo@counts)",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "norm",
+			"extra_data": [
+				"raw",
+				"clean",
+				"filt",
+				"norm"
+			]
+		},
 		{
 			"id": "vB4qNnRxLt9oAy2d",
 			"category": "gn9FXwemlVazWQIo",
@@ -46,16 +80,6 @@
 			"value_type": "string",
 			"default_value": "Group"
 		},
-		{
-			"id": "UA4GuIpVAxdcmHAG",
-			"category": "XqgPq28Eo5VCFSZu",
-			"name": "Count type",
-			"param_name": "count_type",
-			"description": "Type of counts to batch correct. Must be a count type in names(moo@counts)",
-			"type": "text",
-			"value_type": "string",
-			"default_value": "norm"
-		},
 		{
 			"id": "vA3pMmQwKs8nZx1c",
 			"category": "XqgPq28Eo5VCFSZu",
@@ -88,7 +112,7 @@
 		},
 		{
 			"id": "vG9vSsWcQy4tFz7i",
-			"category": "XqgPq28Eo5VCFSZu",
+			"category": "VisGeneral",
 			"name": "Label column name",
 			"param_name": "label_colname",
 			"description": "Column from sample metadata containing labels for plots",
@@ -107,14 +131,227 @@
 			"value_type": "string"
 		},
 		{
-			"id": "vJ2yVvZfTb7wIc0l",
+			"id": "vI1xUuYeSa6vHb9k",
 			"category": "XqgPq28Eo5VCFSZu",
+			"name": "Samples to rename",
+			"param_name": "samples_to_rename",
+			"description": "Sample renaming pairs: old_name:new_name",
+			"help_text": "Separate multiple pairs with commas",
+			"type": "text",
+			"value_type": "string"
+		},
+		{
+			"id": "vJ2yVvZfTb7wIc0l",
+			"category": "VisGeneral",
 			"name": "Colors for plots",
 			"param_name": "colors_for_plots",
-			"description": "Comma-separated list of colors for PCA and histogram",
-			"help_text": "Use color names or hex codes. Leave blank to use defaults",
+			"description": "Comma-separated colors for PCA and histogram. Defaults to the MOSuite palette.",
+			"help_text": "Use color names or hex codes. Supplied colors are used first; if there are more groups than colors, additional colors are generated from the MOSuite palette, with random colors only if that palette is too short.",
 			"type": "text",
-			"value_type": "string"
+			"value_type": "string",
+			"default_value": "#5954d6,#e1562c,#b80058,#00c6f8,#d163e6,#00a76c,#ff9287,#008cf9,#006e00,#796880,#FFA500,#878500"
+		},
+		{
+			"id": "vK3zWwAgUc8xJd1m",
+			"category": "VisPCA",
+			"name": "Add labels to PCA",
+			"param_name": "add_label_to_pca",
+			"description": "Label points on the PCA plot",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "TRUE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
+		},
+		{
+			"id": "vL4aXxBhVd9yKe2n",
+			"category": "VisPCA",
+			"name": "PCA component on x-axis",
+			"param_name": "principal_component_on_x_axis",
+			"description": "Principal component to plot on the x-axis",
+			"type": "text",
+			"value_type": "integer",
+			"default_value": "1"
+		},
+		{
+			"id": "vM5bYyCiWe0zLf3o",
+			"category": "VisPCA",
+			"name": "PCA component on y-axis",
+			"param_name": "principal_component_on_y_axis",
+			"description": "Principal component to plot on the y-axis",
+			"type": "text",
+			"value_type": "integer",
+			"default_value": "2"
+		},
+		{
+			"id": "vN6cZzDjXf1aMg4p",
+			"category": "VisPCA",
+			"name": "Legend position for PCA",
+			"param_name": "legend_position_for_pca",
+			"description": "Legend position for the PCA plot",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "top",
+			"extra_data": [
+				"top",
+				"bottom",
+				"left",
+				"right"
+			]
+		},
+		{
+			"id": "vO7dAaEkYg2bNh5q",
+			"category": "VisPCA",
+			"name": "Label offset x",
+			"param_name": "label_offset_x_",
+			"description": "Label offset x for the PCA plot",
+			"type": "text",
+			"value_type": "number",
+			"default_value": "2"
+		},
+		{
+			"id": "vP8eBbFlZh3cOi6r",
+			"category": "VisPCA",
+			"name": "Label offset y",
+			"param_name": "label_offset_y_",
+			"description": "Label offset y for the PCA plot",
+			"type": "text",
+			"value_type": "number",
+			"default_value": "2"
+		},
+		{
+			"id": "vQ9fCcGmAi4dPj7s",
+			"category": "VisPCA",
+			"name": "Label font size",
+			"param_name": "label_font_size",
+			"description": "Label font size for the PCA plot",
+			"type": "text",
+			"value_type": "number",
+			"default_value": "3"
+		},
+		{
+			"id": "vR0gDdHnBj5eQk8t",
+			"category": "VisPCA",
+			"name": "Point size for PCA",
+			"param_name": "point_size_for_pca",
+			"description": "Point size for the PCA plot",
+			"type": "text",
+			"value_type": "number",
+			"default_value": "3"
+		},
+		{
+			"id": "vS1hEeIoCk6fRl9u",
+			"category": "VisHistogram",
+			"name": "Color histogram by group",
+			"param_name": "color_histogram_by_group",
+			"description": "Color histogram by group instead of sample",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "TRUE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
+		},
+		{
+			"id": "vT2iFfJpDl7gSm0v",
+			"category": "VisHistogram",
+			"name": "Set histogram x-axis min/max",
+			"param_name": "set_min_max_for_x_axis_for_histogram",
+			"description": "Set min/max value for histogram x-axis",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "FALSE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
+		},
+		{
+			"id": "vU3jGgKqEm8hTn1w",
+			"category": "VisHistogram",
+			"name": "Histogram x-axis minimum",
+			"param_name": "minimum_for_x_axis_for_histogram",
+			"description": "x-axis minimum for histogram plot",
+			"type": "text",
+			"value_type": "number",
+			"default_value": "-1"
+		},
+		{
+			"id": "vV4kHhLrFn9iUo2x",
+			"category": "VisHistogram",
+			"name": "Histogram x-axis maximum",
+			"param_name": "maximum_for_x_axis_for_histogram",
+			"description": "x-axis maximum for histogram plot",
+			"type": "text",
+			"value_type": "number",
+			"default_value": "1"
+		},
+		{
+			"id": "vW5lIiMsGo0jVp3y",
+			"category": "VisHistogram",
+			"name": "Legend font size for histogram",
+			"param_name": "legend_font_size_for_histogram",
+			"description": "Legend font size for histogram plot. Leave blank to scale automatically.",
+			"type": "text",
+			"value_type": "number",
+			"default_value": ""
+		},
+		{
+			"id": "vX6mJjNtHp1kWq4z",
+			"category": "VisHistogram",
+			"name": "Legend position for histogram",
+			"param_name": "legend_position_for_histogram",
+			"description": "Legend position for histogram plot",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "top",
+			"extra_data": [
+				"top",
+				"bottom",
+				"left",
+				"right"
+			]
+		},
+		{
+			"id": "vY7nKkOuIq2lXr5a",
+			"category": "VisHistogram",
+			"name": "Histogram legend columns",
+			"param_name": "number_of_histogram_legend_columns",
+			"description": "Number of columns for the histogram legend",
+			"type": "text",
+			"value_type": "integer",
+			"default_value": "6"
+		},
+		{
+			"id": "vZ8oLlPvJr3mYs6b",
+			"category": "VisGeneral",
+			"name": "Plot correlation heatmap",
+			"param_name": "plot_corr_matrix_heatmap",
+			"description": "Plot correlation heatmap",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "TRUE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
+		},
+		{
+			"id": "vAa9pMmQwKs8nZx1c",
+			"category": "VisGeneral",
+			"name": "Interactive plots",
+			"param_name": "interactive_plots",
+			"description": "Create interactive PCA and histogram plots",
+			"type": "list",
+			"value_type": "string",
+			"default_value": "FALSE",
+			"extra_data": [
+				"TRUE",
+				"FALSE"
+			]
 		}
 	],
 	"results": [

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Code Ocean capsule - MOSuite - batch correct counts
 
+## Development version
+
+- Install MOSuite from the `FigOutSync` package branch during capsule setup so the capsule uses the updated batch correction figure-standardization behavior before the next release image is available (#4, @phoman14).
+- Align batch correction PCA and histogram defaults with the MOSuite package defaults (#4, @phoman14).
+- Improved the Code Ocean parameter UI for the batch correct counts capsule (#3, @phoman14).
+
 ## v4.0
 
 - The MOSuite package is now available in `code/MOSuite`. (#2)
@@ -20,4 +26,4 @@ Use MOSuite v0.2.1-dev docker image
 
 Initial release
 
-<https://poc-nci.codeocean.io/capsule/1373453/tree/v1> `dd55143`
+<https://poc-nci.codeocean.io/capsule/1373453/tree/v1> `dd55143`

code/MOSuite/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MOSuite
 Title: R package for differential multi-omics analysis
-Version: 0.3.1
+Version: 0.3.2.9000
 Authors@R: c(
     person("Kelly", "Sovacool", , "kelly.sovacool@nih.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3283-829X")),
@@ -29,7 +29,7 @@ Imports:
     DESeq2,
     dplyr,
     edgeR,
-    ggplot2 (< 4.0.0),
+    ggplot2,
     glue,
     htmlwidgets,
     jsonlite,

code/MOSuite/NEWS.md

@@ -1,8 +1,18 @@
+## MOSuite development version
+
+- Align plot color defaults with the MOSuite Code Ocean capsule defaults while preserving fallback random colors when a requested palette is too short.
+- Improve top and bottom legend wrapping and automatic legend text sizing for PCA and histogram plots with many or long labels.
+- Align PCA and histogram plotting defaults used by `filter_counts()`, `normalize_counts()`, and `batch_correct_counts()` with the affected Code Ocean capsules: MOSuite-filter-counts, MOSuite-normalize-counts, MOSuite-plot-pca-2D, and MOSuite-plot-pca-3D.
+
+## 0.3.2
+
+- Support ggplot2 v4.0.0 for correlation heatmap plots in `filter_counts()`, `normalize_counts()`, and `batch_correct_counts()`. (#205, @copilot, @kelly-sovacool)
+
 ## MOSuite 0.3.1
 
 - Fix recursion error in `plot_venn_diagram()`. (#188, @kelly-sovacool)
 - Fix S7 dispatch argument mismatch in `plot_read_depth()` and `plot_histogram()`. (#200, @copilot, @kelly-sovacool)
-- Fix crash in `remove_low_count_genes()` when `use_group_based_filtering = TRUE`. (#200, @copilot, @kelly-sovacool)
+- Fix bug in `remove_low_count_genes()` when `use_group_based_filtering = TRUE`. (#200, @copilot, @kelly-sovacool)
 - Fix color palette selection to fall back to random colors with a message when the number of categories exceeds the palette maximum. (#204, @copilot, @kelly-sovacool)
 - Update S7 class, generic, and method documentation to use roxygen2 v8.0.0. (#206, #212, @copilot, @kelly-sovacool)
 - A docker container with only MOSuite's dependencies, not MOSuite itself, is now available: <https://hub.docker.com/r/nciccbr/mosuite-minimal>. (#209, @kelly-sovacool)