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Label and hyperlink changes in normalized read count plots
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@skarunan
skarunan committed Feb 7, 2019
1 parent 62e7230 commit acbccf7
Showing 1 changed file with 16 additions and 16 deletions.
32 changes: 16 additions & 16 deletions bin/compPlot.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -31,14 +31,14 @@ COSMO = theme_bw() + theme(plot.title = element_text(size = txtSize, face = "bol
geom_bar(stat="identity")+
facet_wrap(~ region)+scale_y_continuous(trans=log2_trans()) +
scale_fill_viridis(discrete = T, option="D")+
labs(x="Sample", y="Read count (log2)",title=title)+ COSMO + guides(fill=guide_legend(title="Sample"))))
labs(x="Sample", y="Normalized read count (log2)",title=title)+ COSMO + guides(fill=guide_legend(title="Sample"))))
}else{
try(print(ggplot(df,aes(x=samples,y=readCountsNorm,fill=samples)) +
geom_bar(stat="identity") +
facet_wrap(~ region)+
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.45)) +
scale_fill_viridis(discrete=T, option="D")+
labs(x="Sample", y="Read count",title=title)+ COSMO + guides(fill=guide_legend(title="Sample"))))
labs(x="Sample", y="Normalized read count",title=title)+ COSMO + guides(fill=guide_legend(title="Sample"))))
}
}
Expand Down Expand Up @@ -86,14 +86,14 @@ COSMO = theme_bw() + theme(plot.title = element_text(size = txtSize, face = "bol
scale_y_continuous(trans=log2_trans()) +
theme(axis.text.x = element_text(angle = 90, hjust = 0, vjust = 0)) +
scale_fill_viridis(discrete=T, option="D")+
labs(x="Gene/Region", y="Read count (log2) ",title=title)+ COSMO + guides(fill=guide_legend(title="Gene/Region"))))
labs(x="Gene/Region", y="Normalized read count (log2) ",title=title)+ COSMO + guides(fill=guide_legend(title="Gene/Region"))))
}else{
try(print(ggplot(df,aes(x=region,y=readCountsNorm,fill=region)) +
geom_bar(stat="identity") +
facet_wrap(~ samples) +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.45)) +
scale_fill_viridis(discrete=T, option="D")+
labs(x="Gene/Region", y="Read count",title=title)+ COSMO + guides(fill=guide_legend(title="Gene/Region"))))
labs(x="Gene/Region", y="Normalized read count",title=title)+ COSMO + guides(fill=guide_legend(title="Gene/Region"))))
}
Expand Down Expand Up @@ -218,18 +218,18 @@ COSMO = theme_bw() + theme(plot.title = element_text(size = txtSize, face = "bol
try(print(ggplot(dfa, aes(region, readCountsAvg)) + geom_boxplot() + labs(x="Gene/Region", y="Normalized Read Count") + COSMO))
```

### Sample wise comparison of read counts for each gene/region {#Sample}
### Sample wise comparison of normalised read counts for each gene/region {#Sample}

<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#sample-wise-comparison-of-read-counts-for-each-gene-region" target="_blank">See Help</a> &nbsp; [Back To Top](#top)
<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#sample-wise-comparison-of-normalised-read-counts-for-each-gene-region" target="_blank">See Help</a> &nbsp; [Back To Top](#top)

```{r echo=FALSE, fig.height=hval, fig.width=hval}
createSamplePlot(dfa,title="",allowed,plotlog=FALSE)
#createSamplePlot(dfa,title="Sample Comparison",allowed,plotlog=FALSE)
```

### Sample wise comparison of read counts for each gene/region (log2 scale)
### Sample wise comparison of normalised read counts for each gene/region (log2 scale)

<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#sample-wise-comparison-of-read-counts-for-each-gene-region-log2-scale" target="_blank">See Help</a> &nbsp; [Back To Top](#top)
<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#sample-wise-comparison-of-normalised-read-counts-for-each-gene-region-log2-scale" target="_blank">See Help</a> &nbsp; [Back To Top](#top)

```{r echo=FALSE, fig.height=hval, fig.width=hval}
createSamplePlot(dfa,title="",allowed)
Expand Down Expand Up @@ -264,36 +264,36 @@ COSMO = theme_bw() + theme(plot.title = element_text(size = txtSize, face = "bol
#createSampleASRatioPlot(dfa,title="Antisense ratio of samples",allowed)
```

### Gene/Region wise comparsion of read counts for each sample {#Gene}
### Gene/Region wise comparison of normalised read counts for each sample {#Gene}

<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#gene-region-wise-comparsion-of-average-read-counts-for-each-sample" target="_blank">See Help</a> &nbsp; [Back To Top](#top)
<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#gene-region-wise-comparison-of-normalised-read-counts-for-each-sample" target="_blank">See Help</a> &nbsp; [Back To Top](#top)

```{r echo=FALSE, fig.height=hval, fig.width=hval}
createRegionPlot(dfa,title="",allowed)
#createRegionPlot(dfa,title="Gene/Regions Comparison",allowed)
```

### Gene/Region wise comparsion of read counts for each sample (log2 scale)
### Gene/Region wise comparison of normalised read counts for each sample (log2 scale)

<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#gene-region-wise-comparsion-of-average-read-counts-for-each-sample-log2-scale" target="_blank">See Help</a> &nbsp; [Back To Top](#top)
<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#gene-region-wise-comparison-of-normalised-read-counts-for-each-sample-log2-scale" target="_blank">See Help</a> &nbsp; [Back To Top](#top)

```{r echo=FALSE, fig.height=hval, fig.width=hval}
createRegionPlot(dfa,title="",allowed,plotlog=TRUE)
#createRegionPlot(dfa,title="Gene/Regions Comparison in log scale",allowed,plotlog=TRUE)
```

### Gene/Region wise comparsion of TPM for each sample
### Gene/Region wise comparison of TPM for each sample

<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#gene-region-wise-comparsion-of-tpm-for-each-sample" target="_blank">See Help</a> &nbsp; [Back To Top](#top)
<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#gene-region-wise-comparison-of-tpm-for-each-sample" target="_blank">See Help</a> &nbsp; [Back To Top](#top)

```{r echo=FALSE, fig.height=hval, fig.width=hval}
createRegionTPMPlot(dfa,title="",allowed)
#createRegionPlot(dfa,title="Gene/Regions TPM Comparison",allowed)
```

### Gene/Region wise comparsion of TPM for each sample (log2 scale)
### Gene/Region wise comparison of TPM for each sample (log2 scale)

<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#gene-region-wise-comparsion-of-tpm-for-each-sample-log2-scale" target="_blank">See Help</a> &nbsp; [Back To Top](#top)
<a href="https://rapid-doc.readthedocs.io/en/latest/UseCases.html#gene-region-wise-comparison-of-tpm-for-each-sample-log2-scale" target="_blank">See Help</a> &nbsp; [Back To Top](#top)

```{r echo=FALSE, fig.height=hval, fig.width=hval}
createRegionTPMPlot(dfa,title="",allowed,plotlog=TRUE)
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