How to save an 'AI friendly' plot in R when using ggplot2?
When I save a tSNE plot with a large amount of points, I want to convert all the points in the plot to a PNG file while the remainder of the image (axes, labels, all text) remain as vector graphics. How could I do such things?
(I know that the Dimplot function in Seurat package can do this with parameter vector.friendly = TRUE)
r ggplot2
asked Nov 23 '18 at 13:40
李子逸李子逸
142
add a comment |
When I save a tSNE plot with a large amount of points, I want to convert all the points in the plot to a PNG file while the remainder of the image (axes, labels, all text) remain as vector graphics. How could I do such things?
(I know that the Dimplot function in Seurat package can do this with parameter vector.friendly = TRUE)
r ggplot2
asked Nov 23 '18 at 13:40
李子逸李子逸
142
Not sure if there is a ready tool for this, but we could output plot without axis as png image, then plot blank ggplot, then add saved image to the plot.
– zx8754
Nov 23 '18 at 13:47
2
This is whatseurat::dimplotis doing, too, see GitHub - L2450 and see AugmentPlot function.
– zx8754
Nov 23 '18 at 13:55
Any reason why dimplot is not an option?
– Roman Luštrik
Nov 23 '18 at 14:07
Thank you, I think that plot ggplot with axis and text and then add a png image might be the best choice. The reason that not to use dimplot is that dimplot only use seurat object as an input, I want to avoid this.
– 李子逸
Nov 24 '18 at 13:10
add a comment |
When I save a tSNE plot with a large amount of points, I want to convert all the points in the plot to a PNG file while the remainder of the image (axes, labels, all text) remain as vector graphics. How could I do such things?
(I know that the Dimplot function in Seurat package can do this with parameter vector.friendly = TRUE)
r ggplot2
asked Nov 23 '18 at 13:40
李子逸李子逸
142
When I save a tSNE plot with a large amount of points, I want to convert all the points in the plot to a PNG file while the remainder of the image (axes, labels, all text) remain as vector graphics. How could I do such things?
(I know that the Dimplot function in Seurat package can do this with parameter vector.friendly = TRUE)
r ggplot2
r ggplot2
asked Nov 23 '18 at 13:40
李子逸李子逸
142
asked Nov 23 '18 at 13:40
李子逸李子逸
142
asked Nov 23 '18 at 13:40
李子逸李子逸
142
asked Nov 23 '18 at 13:40
李子逸李子逸
142
asked Nov 23 '18 at 13:40
李子逸李子逸
142
142
Not sure if there is a ready tool for this, but we could output plot without axis as png image, then plot blank ggplot, then add saved image to the plot.
– zx8754
Nov 23 '18 at 13:47
2
This is whatseurat::dimplotis doing, too, see GitHub - L2450 and see AugmentPlot function.
– zx8754
Nov 23 '18 at 13:55
Any reason why dimplot is not an option?
– Roman Luštrik
Nov 23 '18 at 14:07
Thank you, I think that plot ggplot with axis and text and then add a png image might be the best choice. The reason that not to use dimplot is that dimplot only use seurat object as an input, I want to avoid this.
– 李子逸
Nov 24 '18 at 13:10
add a comment |
Not sure if there is a ready tool for this, but we could output plot without axis as png image, then plot blank ggplot, then add saved image to the plot.
– zx8754
Nov 23 '18 at 13:47
2
This is whatseurat::dimplotis doing, too, see GitHub - L2450 and see AugmentPlot function.
– zx8754
Nov 23 '18 at 13:55
Any reason why dimplot is not an option?
– Roman Luštrik
Nov 23 '18 at 14:07
Thank you, I think that plot ggplot with axis and text and then add a png image might be the best choice. The reason that not to use dimplot is that dimplot only use seurat object as an input, I want to avoid this.
– 李子逸
Nov 24 '18 at 13:10
Not sure if there is a ready tool for this, but we could output plot without axis as png image, then plot blank ggplot, then add saved image to the plot.
– zx8754
Nov 23 '18 at 13:47
Not sure if there is a ready tool for this, but we could output plot without axis as png image, then plot blank ggplot, then add saved image to the plot.
– zx8754
Nov 23 '18 at 13:47
2
2
This is what
seurat::dimplot is doing, too, see GitHub - L2450 and see AugmentPlot function.– zx8754
Nov 23 '18 at 13:55
This is what
seurat::dimplot is doing, too, see GitHub - L2450 and see AugmentPlot function.– zx8754
Nov 23 '18 at 13:55
Any reason why dimplot is not an option?
– Roman Luštrik
Nov 23 '18 at 14:07
Any reason why dimplot is not an option?
– Roman Luštrik
Nov 23 '18 at 14:07
Thank you, I think that plot ggplot with axis and text and then add a png image might be the best choice. The reason that not to use dimplot is that dimplot only use seurat object as an input, I want to avoid this.
– 李子逸
Nov 24 '18 at 13:10
Thank you, I think that plot ggplot with axis and text and then add a png image might be the best choice. The reason that not to use dimplot is that dimplot only use seurat object as an input, I want to avoid this.
– 李子逸
Nov 24 '18 at 13:10
add a comment |
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Not sure if there is a ready tool for this, but we could output plot without axis as png image, then plot blank ggplot, then add saved image to the plot.
– zx8754
Nov 23 '18 at 13:47
2
This is what
seurat::dimplotis doing, too, see GitHub - L2450 and see AugmentPlot function.– zx8754
Nov 23 '18 at 13:55
Any reason why dimplot is not an option?
– Roman Luštrik
Nov 23 '18 at 14:07
Thank you, I think that plot ggplot with axis and text and then add a png image might be the best choice. The reason that not to use dimplot is that dimplot only use seurat object as an input, I want to avoid this.
– 李子逸
Nov 24 '18 at 13:10