User: mohammedtoufiq91

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Posts by mohammedtoufiq91

<prev • 111 results • page 1 of 12 • next >
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Comment: C: Customize fold change legend values in ComplexHeatmap
... 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 mohammedtoufiq91110
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Comment: C: Customize fold change legend values in ComplexHeatmap
... 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 mohammedtoufiq91110
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Customize fold change legend values in ComplexHeatmap
... 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 ...
R colorramp2 matrix complexheatmap circlize written 9 days ago by mohammedtoufiq91110
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Comment: C: How to visualize Boxplot with using fold change values in ggplot2 in R
... Hi @rpolicastro , thank you very much. ...
written 11 weeks ago by mohammedtoufiq91110
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Comment: C: How to visualize Boxplot with using fold change values in ggplot2 in R
... 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. ![](https://i.imgur.com/IH ...
written 11 weeks ago by mohammedtoufiq91110
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How to visualize Boxplot with using fold change values in ggplot2 in R
... Hi, I have a previously created Boxplots using normalized log2 data using `ggplot2` library in R. Now, I am trying to create the Boxplot using fold change values (example data below) in ggplot2. Could you please assist me how to do the same or provide any useful resources. dput(head(Data)) ...
boxplot R ggplot2 fold change written 11 weeks ago by mohammedtoufiq91110 • updated 11 weeks ago by rpolicastro2.1k
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Comment: C: Batch effect identification using PCA
... Thank you for the comments @Kevin Blighe. ...
written 4 months ago by mohammedtoufiq91110
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Comment: C: Batch effect identification using PCA
... 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 mohammedtoufiq91110
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Batch effect identification using PCA
... 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 ...
targeted assay R pca qrt-pcr batch effect written 4 months ago by mohammedtoufiq91110
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Comment: C: PCA plot on genes and color by batch and plate information
... @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 mohammedtoufiq91110

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Popular Question 8 days ago, created a question with more than 1,000 views. For Identify adapter sequences for trimming from Illumina paired end fastq files
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Popular Question 11 weeks ago, created a question with more than 1,000 views. For Plotting linear trend using the ggplot2 for multiple columns elements
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