Man pages for Japrin/sscVis
simpler single cell RNAseq data Visualization
| auto.colSet | Generate color set automatically |
| auto.point.size | Determine point size automatically |
| collapseEffectSizeLong | collapse effect size, give input table and group variate |
| cor.BLAS | Correlation calculation. use BLAS and data.table to speed up. |
| directEScombi | directional Effect Size combination |
| directEScombiFromLongTable | directional Effect Size combination |
| effectsize | effect size from moderate t test |
| getColorPaletteFromNameContinuous | Determine point size automatically |
| ggGeneOnTSNE | Plot gene expression on tSNE map |
| loginfo | dispaly message with time stamp |
| matrix.waterfall | make the matrix looks like "waterfall" (typically genes... |
| plotBranch | plot branch |
| plotDensity2D | Wrap for plotting 2D density |
| plotDistFromCellInfoTable | plot distribution using cell info table |
| plotDotPlotFromGeneTable | plot a dotplot |
| plotMatrix.simple | plot matrix (typically genes expression) |
| run.cutree | run cutree on rows of the given matrix |
| run.cutreeDynamic | run dynamicTreeCut::cutreeDynamic on rows of the given matrix |
| simple.removeBatchEffect | Modified from limma::removeBatchEffect, a little different... |
| ssc.assay.hclust | sort by hierarchical clustering |
| ssc.assay.zscore | scale the assay per gene |
| ssc.average.cell | calcualte the average expression of cells of each group |
| ssc.average.gene | calcualte the average expression of genes of each cell |
| ssc.build | Build an SingleCellExperiment object |
| ssc.displayName2id | Convert display name (gene symbol) to gene id |
| ssc.downsample | downsample |
| ssc.id2displayName | Convert gene id to display name (gene symbol) |
| ssc.moduleScore | Add module scores for gene expression programs in single... |
| ssc.order | order genes and cells |
| ssc.plot.cor | Plot correlation. |
| ssc.plot.GeneDensity | plot gene expression density |
| ssc.plot.heatmap | plot heatmap |
| ssc.plot.pca | Plot pca result, such as scree plot. |
| ssc.plot.silhouette | Wraper for silhouette() |
| ssc.plot.tsne | Plot on tSNE map |
| ssc.plot.violin | Plot violin |
| ssc.scale | scale the data |
| ssc.toLongTable | convert assay data to long format |
