quick_tutorial.RmdJiayu Zhou. Author, maintainer. +
Jiayu Zhou. Author.
This function is used to visualize the clustering results generated by MICA.
+This function is used to visualize the clustering results +generated by MICA.
Factor, character or numeric, name of the column of MICA
+cluster labels. Default: "clusterID".
A character vector or NULL, colors of the MICA cluster labels. The length of this vector should be same as the number of groups in color_by column. If NULL, the ggplot default colors will be use. Default: NULL.
A character vector or NULL, colors of the MICA cluster
+labels. The length of this vector should be same as the number of groups in
+color_by column. If NULL, the ggplot default colors will be use. Default:
+NULL.
Logical, whether to do the log2(value + 1) transformation. Only valid when color_by is numeric Default: TRUE.
Logical, whether to do the log2(value + 1)
+transformation. Only valid when color_by is numeric Default: TRUE.
Character, name of the columns of x-axis and y-axis coordinates. Default: "UMAP_1", and "UMAP_2".
Character, name of the columns of x-axis and y-axis coordinates.
+Default: "UMAP_1", and "UMAP_2".
left", "top", "bottom" or "none". Default: "right".
+Character, position of legend: "right", "left",
+"top", "bottom" or "none". Default: "right".
Integer, font size of the legend title. Default: 10.
Integer, font size of the legend title. Default: +10.
Integer, font size of the legend text. Default: 8.
Integer, font size of the legend text. Default: +8.
## 1. color-coded by factor or character variable
-p_umap <- MICAplot(input_eset = pbmc14k_log2cpm.eset, color_by = 'clusterID', point.size = 0.1)
-#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'pbmc14k_log2cpm.eset' not found
+
+data(pbmc14k_expression.eset)
+## 1. color-coded by factor or character variable
+p1 <- MICAplot(input_eset = pbmc14k_expression.eset,
+ color_by = "clusterID",
+ X = "UMAP_1", Y = "UMAP_2",
+ point.size = 0.1,
+ fontsize.cluster_label = 6)
## 2. color-coded by numeric variable
-p_umap <- MICAplot(input_eset = pbmc14k_log2cpm.eset, color_by = 'nUMI', do.logTransform = TRUE)
-#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'pbmc14k_log2cpm.eset' not found
+p2 <- MICAplot(input_eset = pbmc14k_expression.eset,
+ color_by = "nUMI",
+ do.logTransform = TRUE,
+ point.size = 0.1)
+#> The values in "nUMI" have been transformed by log2(value + 1). To turn transformation off, set do.logTransform = FALSE.
This function is used to create a folder of the specified project names in the specified project directory as the project space to run scMINER analysis.
-It also creastes 4 subfolers inside of it: "DATA", "MICA", "SJARACNe" and "PLOT".
This function is used to create a folder of the specified
+project names in the specified project directory as the project space to run
+scMINER analysis. It also creastes 4 subfolers inside of it: "DATA",
+"MICA", "SJARACNe" and "PLOT".
It creates a folder of project name and 4 subfolders in the project directory, and returns the path of project space.
+It creates a folder of project name and 4 subfolders in the project +directory, and returns the path of project space.
createProjectSpace(project_dir = "path-to-a-folder", project_name = "PBMC14k")
-#> Error in createProjectSpace(project_dir = "path-to-a-folder", project_name = "PBMC14k"): A folder of the specified project name was found in the specified project directory and it is not empty: path-to-a-folder/PBMC14k.
-#> Please set do.unlink to TRUE to remove the files and subfolder in it, or use another project name.
+ if (FALSE) {
+scminer_dir <- createProjectSpace(project_dir = "path-to-a-folder",
+ project_name = "PBMC14k")
+}
+
## 1. violin plots grouped by clusters (say the column name is 'clusterID')
-p_box <- feature_boxplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), group_by = "clusterID")
+p_box <- feature_boxplot(input_eset = clustered.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ group_by = "clusterID")
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 2. violin plots grouped by cell types (say the column name is 'cellType')
-p_box <- feature_boxplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), group_by = "cellType")
+p_box <- feature_boxplot(input_eset = clustered.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ group_by = "cellType")
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 3. customize the colors to fill the violin plots
-p_box <- feature_boxplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), group_by = "clusterID", colors = c("blue", "red", "green"))
+p_box <- feature_boxplot(input_eset = clustered.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ group_by = "clusterID",
+ colors = c("blue", "red", "green"))
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 4. add jittered points
-p_box <- feature_boxplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), group_by = "clusterID", add_jitter = TRUE, jitter.width = 0.5, jitter.size = 0.5)
+p_box <- feature_boxplot(input_eset = clustered.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ group_by = "clusterID",
+ add_jitter = TRUE,
+ jitter.width = 0.5, jitter.size = 0.5)
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 5. using activity data
-p_box <- feature_boxplot(input_eset = activity_clustered.eset, features = c("CD14_SIG", "CD19_SIG", "CD8A_SIG"), group_by = "clusterID", ylabel_text = "Activity")
+p_box <- feature_boxplot(input_eset = activity_clustered.eset,
+ features = c("CD14_SIG", "CD19_SIG", "CD8A_SIG"),
+ group_by = "clusterID", ylabel_text = "Activity")
#> Error in feature_boxplot(input_eset = activity_clustered.eset, features = c("CD14_SIG", "CD19_SIG", "CD8A_SIG"), group_by = "clusterID", ylabel_text = "Activity"): unused argument (ylabel_text = "Activity")
features_of_interest <- c("CD3D","CD27","IL7R","SELL","CCR7","IL32","GZMA","GZMK","DUSP2","CD8A","GZMH","GZMB","CD79A","CD79B","CD86","CD14")
## 1. the most commonly used command
-p_bubble <- feature_bubbleplot(input_eset = clustered.eset, features = features_of_interest, group_by = "clusterID")
+feature_bubbleplot(input_eset = clustered.eset,
+ features = features_of_interest,
+ group_by = "clusterID")
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 2. customize the colors
-p_bubble <- feature_bubbleplot(input_eset = clustered.eset, features = features_of_interest, group_by = "clusterID", colors = c("lightgrey", "red"))
+feature_bubbleplot(input_eset = clustered.eset,
+ features = features_of_interest,
+ group_by = "clusterID",
+ colors = c("lightgrey", "red"))
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
features_of_interest <- c("CD3D","CD27","IL7R","SELL","CCR7","IL32","GZMA","GZMK","DUSP2","CD8A","GZMH","GZMB","CD79A","CD79B","CD86","CD14")
## 1. the most commonly used command
-feature_heatmap(input_eset = clustered.eset, features = features_of_interest, group_by = "clusterID")
+feature_heatmap(input_eset = clustered.eset,
+ features = features_of_interest,
+ group_by = "clusterID")
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 2. add one more column ('true_label') for cell annotation
-feature_heatmap(input_eset = clustered.eset, features = features_of_interest, group_by = "clusterID", annotation_columns = c("true_label"))
+feature_heatmap(input_eset = clustered.eset,
+ features = features_of_interest,
+ group_by = "clusterID",
+ annotation_columns = c("true_label"))
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 3. scale the data by row
-feature_heatmap(input_eset = clustered.eset, features = features_of_interest, group_by = "clusterID", scale_method = "row")
+feature_heatmap(input_eset = clustered.eset,
+ features = features_of_interest,
+ group_by = "clusterID",
+ scale_method = "row")
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 4. cluster the rows
-feature_heatmap(input_eset = clustered.eset, features = features_of_interest, group_by = "clusterID", cluster_rows = TRUE)
+feature_heatmap(input_eset = clustered.eset,
+ features = features_of_interest,
+ group_by = "clusterID",
+ cluster_rows = TRUE)
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 5. add gaps
-feature_heatmap(input_eset = clustered.eset, features = features_of_interest, group_by = "clusterID", use_gaps.column = TRUE, use_gaps.row = TRUE)
+feature_heatmap(input_eset = clustered.eset,
+ features = features_of_interest,
+ group_by = "clusterID",
+ use_gaps.column = TRUE,
+ use_gaps.row = TRUE)
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 1. scatter plots with UMAP projections
-p_scatter <- feature_scatterplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), location_x = "UMAP_1", location_y = "UMAP_2")
+feature_scatterplot(input_eset = clustered.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ location_x = "UMAP_1", location_y = "UMAP_2")
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 2. scatter plots with t-SNE projections
-p_scatter <- feature_scatterplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), location_x = "tSNE_1", location_y = "tSNE_2")
+feature_scatterplot(input_eset = clustered.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ location_x = "tSNE_1", location_y = "tSNE_2")
#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
## 3. change the point size and font size
-p_scatter <- feature_scatterplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), location_x = "UMAP_1", location_y = "UMAP_2", point.size = 1, fontsize.strip = 12, fontsize.axis = 10)
+feature_scatterplot(input_eset = clustered.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ location_x = "UMAP_1", location_y = "UMAP_2",
+ point.size = 1,
+ fontsize.strip = 12, fontsize.axis = 10)
#> Error in feature_scatterplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), location_x = "UMAP_1", location_y = "UMAP_2", point.size = 1, fontsize.strip = 12, fontsize.axis = 10): argument 7 matches multiple formal arguments
## 1. violin plots grouped by clusters (say the column name is 'clusterID')
-p_vln <- feature_vlnplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), group_by = "clusterID")
-#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
+ data(pbmc14k_expression.eset)
+
+## 1. violin plots grouped by clusters (say the column name is 'clusterID')
+p_vln <- feature_vlnplot(input_eset = pbmc14k_expression.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ group_by = "clusterID")
## 2. violin plots grouped by cell types (say the column name is 'cellType')
-p_vln <- feature_vlnplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), group_by = "cellType")
-#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
+p_vln <- feature_vlnplot(input_eset = pbmc14k_expression.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ group_by = "cellType")
## 3. customize the colors to fill the violin plots
-p_vln <- feature_vlnplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), group_by = "clusterID", colors = c("blue", "red", "green"))
-#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
+p_vln <- feature_vlnplot(input_eset = pbmc14k_expression.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ group_by = "clusterID",
+ colors = c("blue", "red", "green"))
## 4. add jittered points
-p_vln <- feature_vlnplot(input_eset = clustered.eset, features = c("CD14", "CD19", "CD8A"), group_by = "clusterID", add_jitter = TRUE, jitter.width = 0.5, jitter.size = 0.5)
-#> Error in eval(expr, envir, enclos): object 'clustered.eset' not found
+p_vln <- feature_vlnplot(input_eset = pbmc14k_expression.eset,
+ features = c("CD14", "CD19", "CD8A"),
+ group_by = "clusterID",
+ add_jitter = TRUE, jitter.width = 0.5, jitter.size = 0.5)
## 5. using activity data
-p_vln <- feature_vlnplot(input_eset = activity_clustered.eset, features = c("CD14_SIG", "CD19_SIG", "CD8A_SIG"), group_by = "clusterID", ylabel_text = "Activity")
+p_vln <- feature_vlnplot(input_eset = activity_clustered.eset,
+ features = c("CD14_SIG", "CD19_SIG", "CD8A_SIG"),
+ group_by = "clusterID", ylabel_text = "Activity")
#> Error in feature_vlnplot(input_eset = activity_clustered.eset, features = c("CD14_SIG", "CD19_SIG", "CD8A_SIG"), group_by = "clusterID", ylabel_text = "Activity"): unused argument (ylabel_text = "Activity")
filtered.eset <- filterSparseEset(raw.eset) ## filter the input eset using the cutoffs calculated by scMINER.
+ ## 1. using the cutoffs automatically calculated by scMINER
+pbmc14k_filtered.eset <- filterSparseEset(pbmc14k_raw.eset, filter_mode = "auto", filter_type = "both")
#> Checking the availability of the 5 metrics ('nCell', 'nUMI', 'nFeature', 'pctMito', 'pctSpikeIn') used for filtration ...
-#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'fData': object 'raw.eset' not found
-filtered.eset <- filterSparseEset(raw.eset, gene.nCell_min = 10, cell.nUMI_min = 500, cell.nFeature_min = 100, cell.nFeature_max = 5000, cell.pctMito_max = 0.15)
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'fData': object 'pbmc14k_raw.eset' not found
+
+## 2. using the cutoffs manually specified
+pbmc14k_filtered_manual.eset <- filterSparseEset(pbmc14k_raw.eset, filter_mode = "manual", filter_type = "both",
+ gene.nCell_min = 10,
+ cell.nUMI_min = 500,
+ cell.nUMI_max = 6500,
+ cell.nFeature_min = 200,
+ cell.nFeature_max = 2500,
+ cell.pctMito_max = 0.1)
#> Checking the availability of the 5 metrics ('nCell', 'nUMI', 'nFeature', 'pctMito', 'pctSpikeIn') used for filtration ...
-#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'fData': object 'raw.eset' not found
+#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'fData': object 'pbmc14k_raw.eset' not found