Man pages for iaaka/visutils
QC, analyse and visualize visium
| applyTransforms | Apply list of transformations to image |
| bandwidth.nrd.not0 | Identify optimal bandwidth via normal distribution |
| barplotWithText | Plots barplot with text around bar tops |
| calcColSums | Calculates row sums for matrix subsets |
| calcDistance2SpotSet | Calculates distance from each spot to the spot set |
| calcSpotDistance | Calculates matrix of spatial distances between spot centers |
| char2col | Creates palette for character vector |
| col2hex | Transforms colour to hex representation |
| compareSets | Compare two lists of sets |
| cropVisiumImage | Crop image in Seuart Visium object |
| defineJunction | Annotate spots on border between two features |
| dotPlot | Plots matrix as dotPlot |
| enhanceImage | Adjust image brightnes and contrast |
| findTissueBorder | Classifies visium spots according to its position relative to... |
| first2Upper | Capitalize first letter of input text |
| getCenters | Makes one step coarser spot mesh |
| getColoursByDistance | Maps distance matrix into colour space |
| getConsensus | Calculate consensus matrix for list of clusterings |
| getLineWidth | Returns with of line in user coordinates |
| getMaxInxByFirstDD | Find best match between image and RNA counts to deal with... |
| getMeanSpotColor | Extracts mean color of spots |
| getMeanSpotColor1 | Extracts mean color of given spot |
| getNMFcl | Get clusterings from list of nmfs |
| getNMFNormFs | Get function to normalize NMF results |
| getRotations | Return list of 8 possible mirroring/rotations function |
| getSilhouetteStat | Assesses clusterings against distance matrix |
| hist2D | 2D density plot |
| imageWithText | Plot heatmap with numbers |
| isColors | Tests whether value is colour |
| loadVisiumFrom10x | Download Visium dataset from 10x website |
| log10p1 | log10(1+x) |
| makeDistFeatureSampleTable | Summarises feature expression along specified factor and... |
| mergePNG2PFD | Merge multiple png files into pdf |
| mergeSpots | Merge grouped spots |
| myLoad10X_Spatial | Load spaceranger results |
| my.make.unique | Make Character Strings Unique |
| nmfGetBest | Finds best nmf run |
| num2col | Transforms numbers to colours |
| number2bin | Splits numetic vector into equally sized bins |
| overlayColours | Calculate per-row mean colour according to opacity |
| overlayTwoColours | Sums two colours with alpha channel |
| plotArea | Line with confidence interval |
| plotColorAnn | Adds color annotation to plot |
| plotColorLegend | Gradient legend |
| plotColorLegend2 | Gradient legend |
| plotConditionsProfiles | Plot feature profile along distance for multiple conditions |
| plotFeatureProfiles | Plots features profiles |
| plotLine | Plots scatterplot with regression line |
| plotNMFCons | Plots NMF clustering, silhouette and consensuse clustering |
| plotPanelLetter | Add panel label |
| plotPointDensity | Scatterplot wih point density shown by colour |
| plotTD.HM | Plots results of testTDConditions |
| plotVisium | Plot Visium sample |
| plotVisiumHex | Plot Visium as honeycombs |
| plotVisiumImg | Plot Visium sample on top of H&E |
| plotVisiumMultyColours | Plot multiple numerical values (gene expression or cell... |
| pointKde2d | Estimates density at specified 2D points |
| recycle | Recycle vector v along i |
| renameClustsBySize | Rename cluster by size |
| rotateVisium | Rotates Seurat visium slide |
| scaleTo | Scale numeric vector |
| scaleVisiumImage | Resizes H&E image |
| splitSub | Cuts part of delimited text analogous to bash cut |
| symbols.pie | Plots scatter pie |
| testTDConditions | Compare features bewteeb two conditions |
| trimQ | Trim by quantiles |
| weightedColourMeans | Calculate weighted mean colour |
