Dear R Community,
I tried to generate heatmap for a matrix of 1500 columns by 106 rows using the following R script: > pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,border_color=NA) and got the graph (as attached Fig 1) Since the column labels appear very crowded, I tried to increase the cellwidth to stretch the graph horizontally. The idea was to show the graph section by section, but with clear/readable column labels (not overlapped labels). So I typed: > pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,cellwidth=3,cellheight=3,border_color=NA) However, this time I only got middle part of the original heatmap (as attached Fig 2) I wonder if there is way I could output the whole graph after such horizontal stretch. If not, how do I get the left end of the graph. Thank you very much for any inputs! Kind regards, Ace ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. example-graph.pdf (177K) Download Attachment |
> On Sep 18, 2017, at 9:26 AM, Fix Ace via R-help <[hidden email]> wrote: > > Dear R Community, > I tried to generate heatmap for a matrix of 1500 columns by 106 rows using the following R script: >> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,border_color=NA) > and got the graph (as attached Fig 1) > > Since the column labels appear very crowded, I tried to increase the cellwidth to stretch the graph horizontally. The idea was to show the graph section by section, but with clear/readable column labels (not overlapped labels). > So I typed: >> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,cellwidth=3,cellheight=3,border_color=NA) > However, this time I only got middle part of the original heatmap (as attached Fig 2) > I wonder if there is way I could output the whole graph after such horizontal stretch. If not, how do I get the left end of the graph. > Why not define a graphics device that is wider? -- David Winsemius Alameda, CA, USA 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
Thank you so much for the reply! I thought the file would automatically adjust accordingly. But I just checked and found pheatmap does has width as parameter!
Ace On Monday, September 18, 2017 3:00 PM, David Winsemius <[hidden email]> wrote: > On Sep 18, 2017, at 9:26 AM, Fix Ace via R-help <[hidden email]> wrote: > > Dear R Community, > I tried to generate heatmap for a matrix of 1500 columns by 106 rows using the following R script: >> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,border_color=NA) > and got the graph (as attached Fig 1) > > Since the column labels appear very crowded, I tried to increase the cellwidth to stretch the graph horizontally. The idea was to show the graph section by section, but with clear/readable column labels (not overlapped labels). > So I typed: >> pheatmap(tf.vs.DE.1.removeAllZeroCol, fontsize=3,cellwidth=3,cellheight=3,border_color=NA) > However, this time I only got middle part of the original heatmap (as attached Fig 2) > I wonder if there is way I could output the whole graph after such horizontal stretch. If not, how do I get the left end of the graph. > Why not define a graphics device that is wider? -- David Winsemius Alameda, CA, USA 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
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