User: mohammedtoufiq91
mohammedtoufiq91 • 110
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Posts by mohammedtoufiq91
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... I wanted to input (-3,0,6), now I can see in the legend. Thank you so much.
col_fun = circlize::colorRamp2(c(-2,0,2), c("blue", "white", "red"))
pdf("Heatmap.pdf",height = 5, width = 7)
ht=Heatmap(my_matrix,
name = "Fold Change Values",
col = circlize::col ...
written 9 days ago by
mohammedtoufiq91 • 110
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... Hi @ATpoint, thank you for your prompt reply.
I tried running this code, however,
Error in Heatmap(my_matrix, name = "Fold Change Values", col_fun = circlize::colorRamp2(c(-2, :
unused argument (col_fun = circlize::colorRamp2(c(-2, 0, 2), c("blue", "white", "red")))
draw(ht,heatma ...
written 9 days ago by
mohammedtoufiq91 • 110
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... Hi,
I have a question about customizing the fold change legend values applied on a data matrix in R. I am plotting the heatmap on my data matrix using the `library(ComplexHeatmap)` and `library(circlize)`. However, when I try to input values in `col_fun` in the range of (-2,0,2) or even (-2,0,5). I ...
written 9 days ago by
mohammedtoufiq91 • 110
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... Hi @rpolicastro , thank you very much. ...
written 11 weeks ago by
mohammedtoufiq91 • 110
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... Hi @rpolicastro, thank you very much for the inputs.
Another question, I wanted to know if there is a way to draw horizontal lines over the Boxplot to indicate or label the p-value significance values as represented in the example plot or this should be manually created.
 in ggplot2. Could you please assist me how to do the same or provide any useful resources.
dput(head(Data))
...
written 11 weeks ago by
mohammedtoufiq91 • 110
• updated
11 weeks ago by
rpolicastro • 2.1k
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... Thank you for the comments @Kevin Blighe. ...
written 4 months ago by
mohammedtoufiq91 • 110
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... Thank you for the inputs @Kevin Blighe. I will look the annotations for the yellow samples that grouped at the top.
Regarding this, `Evidence against there being a batch effect is illustrated by many blue and yellow samples grouping together`, if the samples are grouped that means it has batch effe ...
written 4 months ago by
mohammedtoufiq91 • 110
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... Hi,
I have a question about batch effect. I used the qRT-PCR transcript targeted assay with around 300 genes with 160 samples (included 30 samples from batch 1 and 130 samples from batch 2). Batch 1 experiment and Batch 2 experiment was performed on different days. I used normalized log2-scale rela ...
written 4 months ago by
mohammedtoufiq91 • 110
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... @RamRS, please find the data below:
head(Neg_Dct_v1)
S1_1 S1_2 S1_3 S1_4 S1_5 S1_6
Batch "Batch_1" "Batch_1" "Batch_1" "Batch_2" "Batch_2" "Batch_2"
Plate "Plate_1" "Plate_2" "Plate_1" "Plate_2" " ...
written 4 months ago by
mohammedtoufiq91 • 110
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