Man pages for Tong-Chen/YSX
For Yishengxin Training
| base_plot_save | Generate suitable output graphics device by file suffix. |
| checkAndInstallPackages | Check and install given packages |
| clusterSampleHeatmap2 | Compute and plot column correlation matrix. Normally used to... |
| clusterSamplePheatmap | Compute and plot column correlation matrix. Normally used to... |
| clusterSampleUpperTriPlot | Compute and plot column correlation matrix. Normally used to... |
| dataFilter | Filter low variance genes by given minimal 'mad' value or... |
| deseq2normalizedExpr | To output normalized results to files named by given... |
| DESeq2_ysx | One step DEseq2 DE genes analysis for salmon output. |
| dh | Transfer day to hours |
| draw_colnames_custom | Pheatmap function only for inner usages |
| enrichCustomizedPathway | Enrichment of customrized pathway or annotation for any... |
| enrichGO_model | GO enrichment for model organism. |
| enrichKEGG_model | KEGG enrichment for model organism. |
| find_coordinates | Pheatmap function only for inner usages |
| flower_plot | Flower plot could be treated as one kind of venn diagram but... |
| flower_plot_inner | Flower plot could be treated as one kind of venn diagram but... |
| generateAbundanceDF | Generate gene expression table or otu abundance table with... |
| generate_color_list | Generate color code |
| get_lower_tri | Get lower triangle of the correlation matrix (from web) |
| get_matched_columns_based_on_value | Detect pairs of columns with same unique values (order does... |
| get_upper_tri | Get upper triangle of the correlation matrix (from web) |
| Matrix2colCorrelation | Get ordered column correlation matrix from input dataframe.... |
| mixedToFloat | Transfer numeric string to numeric. |
| multipleGroupDEgenes | DE genes analysis for multiple groups. |
| normalizedExpr2DistribBoxplot | Plot distribution of normalzied expression to check the... |
| numCheck | Check if given string or vector is all numeric |
| pca_run | Title |
| rankPlot | Rankplot for given column. |
| readscount2deseq | Iniitialize a DESeq2 object from raw reads count matrix. |
| salmon2deseq | Iniitialize a DESeq2 object from salmon output. |
| sp_barplot | Generating bar plot |
| sp_boxplot | Generating box plot |
| sp_corrplot | A visualization of a correlation matrix. |
| sp_current_time | Get current time in strign format |
| sp_dendextend | Hierarchical cluster diagram |
| sp_determine_log_add | Determine the value to add befor log transform. |
| sp_enrichment | Generating enrichment plot |
| sp_EulerDiagrams | Generate Euler diagrams (proposional) |
| sp_get_ggplot_limits | Get the x, y limits of a ggplot2 plot |
| sp_ggplot_add_vline_hline | Add hline or vline for ggplot2 object |
| sp_ggplot_facet | Facet ggplot2 object |
| sp_ggplot_layout | Change common layout of ggplot2 object |
| sp_hclust | Hierarchical cluster diagram |
| sp_histogram | Generating histogram plot |
| sp.is.null | Check Null Object |
| sp_lines | Generating lines plot |
| sp_load_font | Use showtext to load fonts |
| sp_manhattan2_plot | Generating manhattan plot |
| sp_manual_color_ggplot2 | Add manual color assignment for both categorical and... |
| sp_manual_fill_ggplot2 | Add manual fill-color assignment for both categorical and... |
| sp_pca | Generating pca plot |
| sp_pcoa | Generating pcoa plot |
| sp_pheatmap | Generating pheatmap plot |
| sp_raincloud | raincloud |
| sp_read_in_long_wide_matrix | Used to read in long/wide format file or datafrmes. Wide... |
| sp_readTable | Read in data |
| sp_scatterplot | Generating scatter plot |
| sp_set_factor_order | Set factor order of given variable. If 'variable_order' is... |
| sp_string2vector | Transfer color string to vector |
| sp_transfer_one_column | Transfer one column of data. |
| sp_tree_plot | Generate tree file |
| sp_upsetview | Generating upsetView plot |
| sp_vennDiagram | Generating venDiagram plot |
| sp_vennDiagram2 | Generating venDiagram plot |
| sp_vennDiagram3 | Generating venDiagram plot |
| sp_volcano_plot | Generating volcano plot |
| sp_writeTable | Write dataframe to file with names of first column filled. |
| stackVlnPlot | Get stack violin plot for a normal matrix |
| stackVlnSeuratPlot | Get stacked violin plot for seurat object |
| twoGroupDEgenes | DE genes analysis for two groups. |
| value.identical | Return if unique values of two vectors are the same (order... |
| volcanoPlot | Volcano plot |
| waterfalls_plot | Generate waterfall plot using R package waterfalls. |
| WGCNA_coexprNetwork | WGCNA main function. |
| WGCNA_cytoscape | Export WGCNA resullt for cytoscape input edges and nodes. |
| WGCNA_cytoscape_each_module | Output nodes and edges data for each module only.... |
| WGCNA_dataCheck | This is used to read in and check the distribution of WGCNA... |
| WGCNA_dataFilter | Filter data for WGCNA input to increase computing efficiency... |
| WGCNA_filterTrait | Keep samples in trait data the same of exprMat. |
| WGCNA_GeneModuleTraitCoorelation | Genes correlated with both traits an modules. |
| WGCNA_hubgene | Get top x hub genes for each module. |
| WGCNA_MEs_traitCorrelationHeatmap | Heatmap showing correlation among MEs and traits. |
| WGCNA_ModuleGeneTraitHeatmap | Plot gene module relationship and correlation with traits. |
| WGCNA_moduleTraitPlot | Module-trait heatmap |
| WGCNA_onestep | WGCNA onestep |
| WGCNA_readindata | Read in expression matrix and trait data (if possible). |
| WGCNA_sampleClusterDetectOutlier | Sample cluster and outlier detection |
| WGCNA_saveModuleAndMe | Save gene-module relationships, MEs and plot module... |
| WGCNA_softpower | Select soft power, the minimum number to get scale Free... |
| widedataframe2boxplot | Boxplot for wide data frame (normal gene expression table or... |
