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Featureplot legend

Featureplot legend

This function can be used to add legends to plots. Note that a call to the function locator 1 can be used in place of the x and y arguments. They can be specified by keyword or in any way which is accepted by xy. Other objects will be coerced by as. One of these two must be specified for line drawing. Unlike pointsthis can all be specified as a single multi-character string. Must be specified for symbol drawing.

The allowed values are "o" the default and "n". Note that this is only used if bty! Used for text, and provides the default for pt. A value of 0 means left justified, 0. Useful for y-adjustment when labels are plotmath expressions. Should be a single positive number even for a reversed x axis. Defaults to the proper value computed by strwidth legend. Defaults to TRUE if there are points and lines. Arguments xylegend are interpreted in a non-standard way to allow the coordinates to be specified via one or two arguments.

If legend is missing and y is not numeric, it is assumed that the second argument is intended to be legend and that the first argument specifies the coordinates.

The coordinates can be specified in any way which is accepted by xy. If this gives the coordinates of one point, it is used as the top-left coordinate of the rectangle containing the legend. If it gives the coordinates of two points, these specify opposite corners of the rectangle either pair of corners, in any order.

The location may also be specified by setting x to a single keyword from the list "bottomright""bottom""bottomleft""left""topleft""top""topright""right" and "center". This places the legend on the inside of the plot frame at the given location.

featureplot legend

Partial argument matching is used. The optional inset argument specifies how far the legend is inset from the plot margins. If a single value is given, it is used for both margins; if two values are given, the first is used for x - distance, the second for y -distance. Attribute arguments such as colpchltyetc, are recycled if necessary: merge is not. Set entries of lty to 0 or set entries of lwd to NA to suppress lines in corresponding legend entries; set pch values to NA to suppress points.

Points are drawn after lines in order that they can cover the line with their background color pt. Since they are not used for Unicode code points, values are silently omitted, as are NA and "" values. Becker, R.Colors single cells on a dimensional reduction plot according to a 'feature' i. A column name from a DimReduc object corresponding to the cell embedding values e.

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The two colors to form the gradient over. Provide as string vector with the first color corresponding to low values, the second to high. Also accepts a Brewer color scale or vector of colors. Note: this will bin the data into number of colors provided. When blend is TRUEtakes anywhere from colors:. Treated as color for double-negatives, will use default colors 2 and 3 for per-feature expression.

First color used for double-negatives, colors 2 and 3 used for per-feature expression, all others ignored. Boolean determining whether to plot cells in order of expression. Can be useful if cells expressing given feature are getting buried. Vector of minimum and maximum cutoff values for each feature, may specify quantile in the form of 'q ' where ' ' is the quantile eg, 'q1', 'q10'.

Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca. A factor in object metadata to split the feature plot by, pass 'ident' to split by cell identity'; similar to the old FeatureHeatmap. If NULL, all points are circles default. You can specify any cell attribute that can be pulled with FetchData allowing for both different colors and different shapes on cells.

Number of columns to combine multiple feature plots to, ignored if split. Combine plots into a single patchwork ed ggplot object. For the old do. Created by DataCamp. Visualize 'features' on a dimensional reduction plot Colors single cells on a dimensional reduction plot according to a 'feature' i. Community examples Looks like there are no examples yet. Post a new example: Submit your example.

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featureplot legend

I've noticed unexpected behavior when I plot metadata in Seurat3 using FeaturePlot. When I plot these data with FeaturePlot without specifying the color:. I get the expected output which has a color scale If I use custom colors, though the color scale seems to take the index-value of the color array it is contained in:.

I've solved this issue by using ggplot directly on the data, but seems to me like it's not the desired behavior by your function. Hi AidanQuinn. Sorry if the cols parameter is a bit unclear as it tries to handle a lot of cases specifically w.

If you want a continuous gradient scale like that, you can provide the colors corresponding to the min and max and it will create the scale based off those. However, a solution probably closer to what you want with RdBu would be to add the continuous color scale as you would for any ggplot object.

Yeap, that's more or less what I did. Totally makes sense why it's happening, just an unexpected behavior from my end.

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Hi andrewwbutler. I guess this is due to the usage of patchwork. Any idea how to change the color scale for all plots within the plot arrangement? Hi christianholland. For more details on this topic, please see the patchwork docs particularly the "Modifying everything" section here. We use optional third-party analytics cookies to understand how you use GitHub.Colors single cells on a dimensional reduction plot according to a 'feature' i. A column name from a DimReduc object corresponding to the cell embedding values e.

The two colors to form the gradient over. Provide as string vector with the first color corresponding to low values, the second to high. Also accepts a Brewer color scale or vector of colors. Note: this will bin the data into number of colors provided.

When blend is TRUEtakes anywhere from colors:. Treated as color for double-negatives, will use default colors 2 and 3 for per-feature expression.

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First color used for double-negatives, colors 2 and 3 used for per-feature expression, all others ignored. Boolean determining whether to plot cells in order of expression. Can be useful if cells expressing given feature are getting buried. Vector of minimum and maximum cutoff values for each feature, may specify quantile in the form of 'q ' where ' ' is the quantile eg, 'q1', 'q10'. Which dimensionality reduction to use.

If not specified, first searches for umap, then tsne, then pca. A factor in object metadata to split the feature plot by, pass 'ident' to split by cell identity'; similar to the old FeatureHeatmap.

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If NULL, all points are circles default. You can specify any cell attribute that can be pulled with FetchData allowing for both different colors and different shapes on cells.

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Number of columns to combine multiple feature plots to, ignored if split. Redundant with order. This argument is being deprecated. Please use order instead. Combine plots into a single patchworked ggplot object. For the old do. For more information on customizing the embed code, read Embedding Snippets. Functions Source code Man pages R Description Colors single cells on a dimensional reduction plot according to a 'feature' i.

R Package Documentation rdrr. We want your feedback! Note that we can't provide technical support on individual packages. You should contact the package authors for that. Tweet to rdrrHQ. GitHub issue tracker. Personal blog.

What can we improve? The page or its content looks wrong. I can't find what I'm looking for. I have a suggestion. Extra info optional.Documentation Help Center. For the labels, the legend uses the text from the DisplayName properties of the data series. If the DisplayName property is empty, then the legend uses a label of the form 'dataN'. The legend automatically updates when you add or delete data series from the axes. This command creates a legend for the current axes or chart returned by gca.

If the current axes are empty, then the legend is empty. If axes do not exist, then this command creates them.

FeaturePlot

Specify the labels as a list of character vectors or strings, such as legend 'Jan','Feb','Mar'. Specify subset as a vector of graphics objects.

featureplot legend

You can specify subset before specifying the labels or with no other input arguments. Specify the target as the first input argument. For example, 'Location','northeast' positions the legend in the upper right corner of the axes. Specify the location after other input arguments. The default for ornt is 'vertical'which stacks the items vertically. The default for bkgd is 'boxon'which displays the legend background and outline.

Use lgd to query and set properties of the legend after it is created.

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For a list of properties, see Legend Properties. Plot two lines and add a legend to the current axes. Specify the legend labels as input arguments to the legend function. If you add or delete a data series from the axes, the legend updates accordingly. Control the label for the new data series by setting the DisplayName property as a name-value pair during creation. If you do not specify a label, then the legend uses a label of the form 'dataN'.

Note: If you do not want the legend to automatically update when data series are added to or removed from the axes, then set the AutoUpdate property of the legend to 'off'. Starting in Rb, you can display a tiling of plots using the tiledlayout and nexttile functions. Call the tiledlayout function to create a 2-by-1 tiled chart layout. Call the nexttile function to create the axes objects ax1 and ax2. Plot random data in each axes.

Add a legend to the upper plot by specifying ax1 as the first input argument to legend. Plot two lines. Specify the legend labels during the plotting commands by setting the DisplayName property to the desired text.Description Usage Arguments Value. Colors single cells on a dimensional reduction plot according to a 'feature' i.

Vector of minimum cutoff values for each feature, may specify quantile in the form of 'q ' where ' ' is the quantile eg, 1, Vector of maximum cutoff values for each feature, may specify quantile in the form of 'q ' where ' ' is the quantile eg, 1, The two colors to form the gradient over.

Provide as string vector with the first color corresponding to low values, the second to high. Also accepts a Brewer color scale or vector of colors.

Note: this will bin the data into number of colors provided. Data to add to the hover, pass a character vector of features to add.

R legend function

Defaults to cell name and identity. Pass 'NULL' to remove extra data. Which dimensionality reduction to use. Default is "tsne", can also be "pca", or "ica", assuming these are precomputed. For more information on customizing the embed code, read Embedding Snippets.

Functions Source code Man pages FeaturePlot objectfeatures. R Package Documentation rdrr. We want your feedback! Note that we can't provide technical support on individual packages.Documentation Help Center.

Change Legend Title in ggplot2 (2 Example Codes) | Modify Text of ggplot Legends

Legends are a useful way to label data series plotted on a graph. These examples show how to create a legend and make some common modifications, such as changing the location, setting the font size, and adding a title. You also can create a legend with multiple columns or create a legend for a subset of the plotted data. Create a figure with a line chart and a scatter chart.

Add a legend with a description for each chart. Specify the legend labels as inputs to the legend function. Alternatively, you can specify the legend labels using the DisplayName property.

Set the DisplayName property as a name-value pair when calling the plotting functions. Then, call the legend command to create the legend.

Legends automatically update when you add or delete a data series. If you add more data to the axes, use the DisplayName property to specify the labels.

If you do not set the DisplayName property, then the legend uses a label of the form 'dataN'. The legend function creates a Legend object. L egend objects have properties that you can use to customize the appearance of the legend, such as the LocationOrientationFontSizeand Title properties.

For a full list, see Legend Properties. Use name-value pairs in the legend command. Use the Legend object. Then, use lgd with dot notation to set properties, such as lgd. Specify the legend location and orientation by setting the Location and Orientation properties as name-value pairs. Set the location to one of the eight cardinal or intercardinal directions, in this case, 'northwest'.

Set the orientation to 'vertical' the default or 'horizontal'as in this case. Specify the labels in a cell array.