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plotHeatmaps.Rd 5.86 KB
 fsoubes committed Oct 09, 2018 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 % Generated by roxygen2: do not edit by hand % Please edit documentation in R/compat.R, R/heatmtruncated.R \name{plotHeatmaps} \alias{plotHeatmaps} \alias{plotHeatmaps} \title{plotHeatmaps is a function that create a false color image with a dendogram added to the left side and the top} \usage{ plotHeatmaps(exprData, groups, workingPath = getwd(), fileType = "png", cexcol = 1.5, cexrow = 1.5, colOrder = NULL, labrow = F, na.color = "black", scale = "row", rowv = list4, ColvOrd = list3, gpcol = list5, gpcolr = list6, distfunTRIX = list2, RowSideColor = c("gray25", "gray75"), palette.col = NULL, margins = c(8, 8), my_palette = colorRampPalette(c("green", "black", "red"))(n = 75), mycex = 0.6, mypal = test, colid = NULL, showcol = T, showrow = F, notplot = F, geneSet = list7, genename = csvf, height = list8, rastering = myras) plotHeatmaps(exprData, groups, workingPath = getwd(), fileType = "png", cexcol = 1.5, cexrow = 1.5, colOrder = NULL, labrow = F, na.color = "black", scale = "row", rowv = list4, ColvOrd = list3, gpcol = list5, gpcolr = list6, distfunTRIX = list2, RowSideColor = c("gray25", "gray75"), palette.col = NULL, margins = c(8, 8), my_palette = colorRampPalette(c("green", "black", "red"))(n = 75), mycex = 0.6, mypal = test, colid = NULL, showcol = T, showrow = F, notplot = F, geneSet = list7, genename = csvf, height = list8, rastering = myras) } \arguments{ \item{exprData}{a data frame with all the individuals selected} \item{groups}{a data frame with the corresponding groups} \item{workingPath}{an access path} \item{fileType}{a character value which extension corresponds to different file types} \item{cexcol}{a positive numbers, used as cex.axis in for the row or column axis labeling} \item{cexrow}{a positive numbers, used as cex.axis in for the row or column axis labeling} \item{colOrder}{a positive numbers, used as cex.axis in for the row or column axis labeling} \item{labrow}{a character vectors with row and column labels to use} \item{na.color}{color to use for missing value} \item{scale}{a character indicating if the values should be centered and scaled in either the row direction or the column direction, or none} \item{rowv}{dendogram object} \item{gpcol}{matrix with colors associated to each groups} \item{gpcolr}{matrix with gray color depending on the clusters} \item{distfunTRIX}{function that computes whether euclidian or pearson for Hierarchical Clustering} \item{RowSideColor}{a character vector of length nrow containing the color names for a vertical side bar that may be used to annotate the rows of x.} \item{palette.col}{NULL} \item{margins}{a numeric vector of length 2 containing the margins (see par(mar= *)) for column and row names, respectively.} \item{my_palette}{a character vetor of length 17} \item{mycex}{a numeric value which aim is to change the size of the legend} \item{mypal}{a character vetor of length 17} \item{colid}{a character vectors with row and column labels to use; default NULL} \item{showcol}{a boolean value used to hide or show the colnames} \item{showrow}{a boolean value used to hide or show the rownames} \item{notplot}{boolean calling or not the dev.off method} \item{geneSet}{a data frame with the indexes corresponding to the sigificant genes} \item{genename}{a data frame list corresponding to the gene names} \item{k}{a numeric value which aim is to defined the treshold value to cut the dendogram} \item{hclustGenes}{a function used to compute the hierarchical clustering when Rowv or Colv are not dendrograms} \item{meanGrp}{a boolean value to computes the mean for each groups; default = F} \item{plotRowSideColor}{a boolean value that colors or not the rows side} \item{Rowdistfun}{a function used to compute the distance for the rows} \item{Coldistfun}{a function used to compute the distance for the columns} \item{exprData}{data frame with all the individuals selected} \item{geneSet}{data frame with the indexes corresponding to the sigificant genes} \item{groups}{data frame with the corresponding groups} \item{workingPath}{an access path} \item{k}{numeric value which aim is to defined the treshold value to cut the dendogram} \item{fileType}{character value which extension corresponds to different file types} \item{cexcol}{positive numbers, used as cex.axis in for the row or column axis labeling} \item{cexrow}{positive numbers, used as cex.axis in for the row or column axis labeling} \item{colOrder}{positive numbers, used as cex.axis in for the row or column axis labeling} \item{labrow}{character vectors with row and column labels to use} \item{na.color}{color to use for missing value} \item{scale}{character indicating if the values should be centered and scaled in either the row direction or the column direction, or none} \item{ColOrd}{positive numbers, used as cex.axis in for the row or column axis labeling} \item{RowSideColor}{a character vector of length nrow containing the color names for a vertical side bar that may be used to annotate the rows of x.} \item{palette.col}{NULL} \item{margins}{numeric vector of length 2 containing the margins (see par(mar= *)) for column and row names, respectively.} \item{my_palette}{a character vetor of length 17} \item{mycex}{numeric value which aim is to change the size of the legend} \item{mypal}{character vetor of length 17} \item{colid}{character vectors with row and column labels to use; default NULL} \item{showcol}{boolean value used to hide or show the colnames} \item{showrow}{boolean value used to hide or show the rownames} \item{genename}{data frame list corresponding to the gene names} } \value{ an heatmap object data frame with the cluster and the corresponding genes } \description{ plotHeatmaps is a function that create a false color image with a dendogram added to the left side and the top plotHeatmaps is a function that creates a false color image with a dendogram added to the left side and the top }