Acid Genomics Plot Functions and Themes
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Documentation for package ‘AcidPlots’ version 0.7.3
Help Pages
-- A --
| acid_discrete_coord_flip | Flip coordinates |
| acid_geom_abline | Reference line |
| acid_geom_bar | Bar chart |
| acid_geom_label | Text label |
| acid_geom_label_average | Average labels |
| acid_geom_label_repel | Repulsive textual annotations |
| acid_pretty_breaks | Pretty breaks that resemble the base plotting engine |
| acid_scale_color_continuous | Automatic color/fill scales to use with ggplot object |
| acid_scale_color_discrete | Automatic color/fill scales to use with ggplot object |
| acid_scale_color_synesthesia_c | Synesthesia color palette |
| acid_scale_color_synesthesia_d | Synesthesia color palette |
| acid_scale_fill_continuous | Automatic color/fill scales to use with ggplot object |
| acid_scale_fill_discrete | Automatic color/fill scales to use with ggplot object |
| acid_scale_fill_synesthesia_c | Synesthesia color palette |
| acid_scale_fill_synesthesia_d | Synesthesia color palette |
| acid_scale_y_continuous_nopad | Remove Y axis padding |
| acid_theme_dark | ggplot2 themes |
| acid_theme_dracula | ggplot2 themes |
| acid_theme_light | ggplot2 themes |
| autoScale | Automatic color/fill scales to use with ggplot object |
-- B --
| blueYellow | Hex color gradient generator |
-- D --
| darkPalette | Color palettes |
| draculaPalette | Color palettes |
-- G --
| gradient | Hex color gradient generator |
-- I --
| iOSDarkPalette | Color palettes |
| iOSLightPalette | Color palettes |
-- L --
| lightPalette | Color palettes |
-- M --
| macOSDarkPalette | Color palettes |
| macOSLightPalette | Color palettes |
| matchLabels | Match ggplot2 labels |
-- P --
| palettes | Color palettes |
| plotBarcodeRanks | Plot barcode ranks |
| plotBarcodeRanks-method | Plot barcode ranks |
| plotCellCounts | Plot cell counts |
| plotCellCounts-method | Plot cell counts |
| plotCellCountsPerCluster | Plot cell counts per cluster |
| plotCellCountsPerCluster-method | Plot cell counts per cluster |
| plotCellTypesPerCluster | Plot cell types per cluster |
| plotCellTypesPerCluster-method | Plot cell types per cluster |
| plotCorrelation | Correlation X-Y scatterplot |
| plotCorrelation-method | Correlation X-Y scatterplot |
| plotCorrelationHeatmap | Correlation heatmap |
| plotCorrelationHeatmap-method | Correlation heatmap |
| plotCounts | Plot counts |
| plotCounts-method | Plot counts |
| plotCountsCorrelation | Plot counts correlation |
| plotCountsCorrelation-method | Plot counts correlation |
| plotCountsCorrelationHeatmap | Plot counts correlation heatmap |
| plotCountsCorrelationHeatmap-method | Plot counts correlation heatmap |
| plotCountsPerBiotype | Plot counts per biotype |
| plotCountsPerBiotype-method | Plot counts per biotype |
| plotCountsPerBroadClass | Plot counts per biotype |
| plotCountsPerBroadClass-method | Plot counts per biotype |
| plotCountsPerCell | Plot counts per cell |
| plotCountsPerCell-method | Plot counts per cell |
| plotCountsPerFeature | Plot counts per feature |
| plotCountsPerFeature-method | Plot counts per feature |
| plotCountsVsFeatures | Plot count and feature correlation |
| plotCountsVsFeatures-method | Plot count and feature correlation |
| plotDots | Plot counts |
| plotDots-method | Plot counts |
| plotFeature | Plot feature |
| plotFeature-method | Plot feature |
| plotFeaturesDetected | Plot features detected |
| plotFeaturesDetected-method | Plot features detected |
| plotFeaturesPerCell | Plot features per cell |
| plotFeaturesPerCell-method | Plot features per cell |
| plotGenderMarkers | Plot sexually dimorphic gender marker genes |
| plotGenderMarkers-method | Plot sexually dimorphic gender marker genes |
| plotHeatmap | Heatmap |
| plotHeatmap-method | Heatmap |
| plotKnownMarkers | Plot known markers |
| plotKnownMarkers-method | Plot known markers |
| plotMarker | Plot cell-type-specific gene markers |
| plotMarker-method | Plot cell-type-specific gene markers |
| plotMitoRatio | Plot mitochondrial transcript abundance |
| plotMitoRatio-method | Plot mitochondrial transcript abundance |
| plotMitoVsCoding | Plot mitochondrial vs. coding counts |
| plotMitoVsCoding-method | Plot mitochondrial vs. coding counts |
| plotNovelty | Plot novelty score |
| plotNovelty-method | Plot novelty score |
| plotPca | Plot reduced dimensions |
| plotPca-method | Plot reduced dimensions |
| plotQc | Quality control |
| plotQc-method | Quality control |
| plotQuantileHeatmap | Quantile heatmap |
| plotQuantileHeatmap-method | Quantile heatmap |
| plotReducedDim | Plot reduced dimensions |
| plotReducedDim-method | Plot reduced dimensions |
| plotStackedBarPlot | Plot stacked bar plot |
| plotStackedBarPlot-method | Plot stacked bar plot |
| plotSums | Plot row or column sums |
| plotSums-method | Plot row or column sums |
| plotTotalCounts | Plot total read counts |
| plotTotalCounts-method | Plot total read counts |
| plotTsne | Plot reduced dimensions |
| plotTsne-method | Plot reduced dimensions |
| plotUmap | Plot reduced dimensions |
| plotUmap-method | Plot reduced dimensions |
| plotUpset | UpSet plot |
| plotUpset-method | UpSet plot |
| plotViolin | Plot counts |
| plotViolin-method | Plot counts |
| plotWaterfall | Plot waterfall |
| plotWaterfall-method | Plot waterfall |
| plotZerosVsDepth | Plot percentage of zeros vs. library depth |
| plotZerosVsDepth-method | Plot percentage of zeros vs. library depth |
| purpleOrange | Hex color gradient generator |
-- S --
| scale_colour_synesthesia_c | Synesthesia color palette |
| scale_colour_synesthesia_d | Synesthesia color palette |
| synesthesia | Synesthesia color palette |
| synesthesia_pal | Synesthesia color palette |
-- T --
| themes | ggplot2 themes |