labeledHeatmap(WGCNA)
labeledHeatmap()所属R语言包：WGCNA
Produce a labeled heatmap plot
标记HeatMap在图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plots a heatmap plot with color legend, row and column annotation, and optional text within th heatmap.
绘制热图图与传奇的色彩，行和列注释，和可选的文字在日热图。
用法----------Usage----------
labeledHeatmap(
Matrix,
xLabels, yLabels = NULL,
xSymbols = NULL, ySymbols = NULL,
colorLabels = NULL,
xColorLabels = FALSE, yColorLabels = FALSE,
checkColorsValid = TRUE,
invertColors = FALSE,
setStdMargins = TRUE,
xLabelsPosition = "bottom",
xLabelsAngle = 45,
xLabelsAdj = 1,
xColorWidth = 0.05,
yColorWidth = 0.05,
colors = NULL,
textMatrix = NULL,
cex.text = NULL, cex.lab = NULL,
cex.lab.x = cex.lab,
cex.lab.y = cex.lab,
colors.lab.x = 1,
colors.lab.y = 1,
plotLegend = TRUE, ...)
参数----------Arguments----------
参数：Matrix
numerical matrix to be plotted in the heatmap.
要绘制的数值矩阵的热图。
参数：xLabels
labels for the columns. See Details.
列的标签。查看详细信息。
参数：yLabels
labels for the rows. See Details.
行的标签。查看详细信息。
参数：xSymbols
additional labels used when xLabels are interpreted as colors. See Details.
额外的标签时使用xLabels被解释为颜色。查看详细信息。
参数：ySymbols
additional labels used when yLabels are interpreted as colors. See Details.
额外的标签时使用yLabels被解释为颜色。查看详细信息。
参数：colorLabels
logical: should xLabels and yLabels be interpreted as colors? If given, overrides xColorLabels and yColorLabels below.
逻辑：应xLabels和yLabels被解释为颜色？如果给定的，覆盖xColorLabels和yColorLabels下面。
参数：xColorLabels
logical: should xLabels be interpreted as colors?
逻辑：应该xLabels地被解释为颜色？
参数：yColorLabels
logical: should yLabels be interpreted as colors?
逻辑：应该yLabels地被解释为颜色？
参数：checkColorsValid
logical: should given colors be checked for validity against the output of colors() ? If this argument is FALSE, invalid color specification will trigger an error.
符合逻辑的：给定的颜色应该被检查的有效性，对输出的colors()？如果这种说法是FALSE，无效的颜色规格将触发一个错误。
参数：invertColors
logical: should the color order be inverted?
逻辑：应的颜色顺序被倒置呢？
参数：setStdMargins
logical: should standard margins be set before calling the plot function? Standard margins depend on colorLabels: they are wider for text labels and narrower for color labels. The defaults are static, that is the function does not attempt to guess the optimal margins.
逻辑：标准页边距设置，然后再调用绘图功能？标准的利润依赖于colorLabels：他们是更广泛的和更窄的彩色标签的文本标签。默认值是静态的，是功能不试图猜测的最佳利润。
参数：xLabelsPosition
a character string specifying the position of labels for the columns. Recognized values are (unique abbreviations of) "top", "bottom".
一个字符串指定位置的列标签。可识别的值是（）"top", "bottom"唯一的缩写。
参数：xLabelsAngle
angle by which the column labels should be rotated.
角列标签应该是旋转。
参数：xLabelsAdj
justification parameter for column labels. See par and the description of parameter "adj".
理由参数列标签。见par和参数"adj"的描述。
参数：xColorWidth
width of the color labels for the x axis expressed as a fraction of the smaller of the range of the x and y axis.
表示为x轴的颜色标签的宽度的一小部分的小的范围内的x和y轴。
参数：yColorWidth
width of the color labels for the y axis expressed as a fraction of the smaller of the range of the x and y axis.
表示为y轴的颜色标签的一小部分的小的范围内的x和y轴的宽度。
参数：colors
color pallette to be used in the heatmap. Defaults to heat.colors.
颜色帕莱特要使用在热图。默认为heat.colors的。
参数：textMatrix
optional matrix of text entries of the same dimensions as Matrix.
可选矩阵的文本条目相同的尺寸，Matrix。
参数：cex.text
character expansion factor for textMatrix.
字符膨胀系数textMatrix。
参数：cex.lab
character expansion factor for text labels labeling the axes.
字符文本标签标记轴的膨胀系数。
参数：cex.lab.x
character expansion factor for text labels labeling the x axis. Overrides cex.lab above.
对于x轴的文本标签标记的字符的扩展系数。覆盖cex.lab以上。
参数：cex.lab.y
character expansion factor for text labels labeling the y axis. Overrides cex.lab above.
字符膨胀系数为y轴标签的文本标签。覆盖cex.lab以上。
参数：colors.lab.x
colors for character labels or symbols along x axis.
沿x轴的字符标签或符号的颜色。
参数：colors.lab.y
colors for character labels or symbols along y axis.
沿y轴的的字符标签或符号的颜色。
参数：plotLegend
logical: should a color legend be plotted?
逻辑：一个传奇的色彩绘制？
参数：...
other arguments to function heatmap.
其它参数的函数heatmap。
Details
详细信息----------Details----------
The function basically plots a standard heatmap plot of the given Matrix and embellishes it with row and column labels and/or with text within the heatmap entries. Row and column labels can be either character strings or color squares, or both.
功能基本绘制标准热图图的给定Matrix和美化它的行和列标签和/或HeatMap在项目内的文字。行和列标签可以是字符串或彩色正方形，或两者。
To get simple text labels, use colorLabels=FALSE and pass the desired row and column labels in yLabels and xLabels, respectively.
为了得到简单的文字标签，使用colorLabels=FALSE“，并通过所需的行和列标签，分别在yLabels和xLabels。
To label rows and columns by color squares, use colorLabels=TRUE; yLabels and xLabels are then expected to represent valid colors. For reasons of compatibility with other functions, each entry in yLabels and xLabels is expected to consist of a color designation preceded by 2 characters: an example would be MEturquoise. The first two characters can be arbitrary, they are stripped. Any labels that do not represent valid colors will be considered text labels and printed in full, allowing the user to mix text and color labels.
标签的行和列的颜色方块，使用colorLabels=TRUEyLabels和xLabels，然后代表有效颜色。出于兼容性等功能，每个条目中yLabels和xLabels预计将包括：一个例子是前面2个字符的颜色指定MEturquoise。前两个字符可以是任意的，他们会被删除。任何标签不表示有效的颜色将被视为文本标签和印在充分，允许用户混合文本和彩色标签。
It is also possible to label rows and columns by both color squares and additional text annotation. To achieve this, use the above technique to get color labels and, additionally, pass the desired text annotation in the xSymbols and ySymbols arguments.
它也可以将标签彩色广场和额外的文本注释的行和列。要做到这一点，使用上述技术，彩色标签，另外，通过xSymbols和ySymbols参数所需的文本注释。
值----------Value----------
None.
无。
（作者）----------Author(s)----------
Peter Langfelder
参见----------See Also----------
heatmap, colors
heatmap，colors
实例----------Examples----------
# This example illustrates 4 main ways of annotating columns and rows of a heatmap.[这个例子说明了注释的行和列的热图的4个主要途径。]
# Copy and paste the whole example into an R session with an interactive plot window;[整个示例复制并粘贴到R会话的交互式绘图窗口;]
# alternatively, you may replace the command sizeGrWindow below by opening another graphical device such[另外，你也可以取代下面的命令sizeGrWindow，打开另一个图形设备]
# as pdf.[为PDF。]
# Generate a matrix to be plotted[生成矩阵被绘制]
nCol = 8; nRow = 7;
mat = matrix(runif(nCol*nRow, min = -1, max = 1), nRow, nCol);
rowColors = standardColors(nRow);
colColors = standardColors(nRow + nCol)[(nRow+1) nRow + nCol)];
rowColors;
colColors;
sizeGrWindow(9,7)
par(mfrow = c(2,2))
par(mar = c(4, 5, 4, 6));
# Label rows and columns by text:[标签文本的行和列：]
labeledHeatmap(mat, xLabels = colColors, yLabels = rowColors,
colors = greenWhiteRed(50),
setStdMargins = FALSE,
textMatrix = signif(mat, 2),
main = "Text-labeled heatmap");
# Label rows and columns by colors:[标签的行和列的颜色：]
rowLabels = paste("ME", rowColors, sep="");
colLabels = paste("ME", colColors, sep="");
labeledHeatmap(mat, xLabels = colLabels, yLabels = rowLabels,
colorLabels = TRUE,
colors = greenWhiteRed(50),
setStdMargins = FALSE,
textMatrix = signif(mat, 2),
main = "Color-labeled heatmap");
# Mix text and color labels:[混合文本和彩色标签：]
rowLabels[3] = "Row 3";
colLabels[1] = "Column 1";
labeledHeatmap(mat, xLabels = colLabels, yLabels = rowLabels,
colorLabels = TRUE,
colors = greenWhiteRed(50),
setStdMargins = FALSE,
textMatrix = signif(mat, 2),
main = "Mix-labeled heatmap");
# Color labels and additional text labels[彩色标签及其他文本标签]
rowLabels = paste("ME", rowColors, sep="");
colLabels = paste("ME", colColors, sep="");
extraRowLabels = paste("Row", c(1:nRow));
extraColLabels = paste("Column", c(1:nCol));
# Extend margins to fit all labels[扩展的利润，以适应所有的标签]
par(mar = c(6, 6, 4, 6));
labeledHeatmap(mat, xLabels = colLabels, yLabels = rowLabels,
xSymbols = extraColLabels,
ySymbols = extraRowLabels,
colorLabels = TRUE,
colors = greenWhiteRed(50),
setStdMargins = FALSE,
textMatrix = signif(mat, 2),
main = "Text- + color-labeled heatmap");
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-10-1 21:15:50
